made ws warning dialog optional, and fixed its wording (JAL-693)

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index d666b01..48837ff 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -127,6 +127,8 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
  * respond to selections made in other alignments containing the same sequences.
  * </li>
+ * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
+ * warning dialog box is displayed.</li>
  * 
  * <li></li>
  * 

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index d263e88..6912e19 100755 (executable)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -2179,32 +2179,42 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    */
   protected void JalviewServicesChanged(PropertyChangeEvent evt)
   {
-    if (evt.getNewValue() instanceof Vector)
+    if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector)
     {
       final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
               .getErrorMessages();
       if (ermsg != null)
       {
-        if (serviceChangedDialog == null)
+        if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true))
         {
-          // only run if we aren't already displaying one of these.
-          javax.swing.SwingUtilities
-                  .invokeLater(serviceChangedDialog = new Runnable()
-                  {
-                    public void run()
-                    {
+          if (serviceChangedDialog == null)
 
-                      JOptionPane
-                              .showInternalMessageDialog(
-                                      Desktop.desktop,
-                                      ermsg
-                                              + "\nPlease check the web services preferences.\n",
-                                      "Preferences Problem",
-                                      JOptionPane.WARNING_MESSAGE);
-                      serviceChangedDialog = null;
-
-                    }
-                  });
+          {
+            // only run if we aren't already displaying one of these.
+            javax.swing.SwingUtilities
+                    .invokeLater(serviceChangedDialog = new Runnable()
+                    {
+                      public void run()
+                      {
+
+                        JOptionPane
+                                .showInternalMessageDialog(
+                                        Desktop.desktop,
+                                        ermsg
+                                                + "It may be that you have invalid JABA URLs\nin your web service preferences.\n\nGo to the Web services tab of the\nTools->Preferences dialog box to change them.\n",
+                                        "Preferences Problem",
+                                        JOptionPane.WARNING_MESSAGE);
+                        serviceChangedDialog = null;
+
+                      }
+                    });
+          }
+        }
+        else
+        {
+          Cache.log
+                  .error("Errors reported by JABA discovery service. Check web services preferences.\n"
+                          + ermsg);
         }
       }
     }

diff --git a/src/jalview/gui/WsPreferences.java b/src/jalview/gui/WsPreferences.java
index 4fb8e6e..ff149c1 100644 (file)
--- a/src/jalview/gui/WsPreferences.java
+++ b/src/jalview/gui/WsPreferences.java
@@ -19,6 +19,7 @@ package jalview.gui;
 
 import java.awt.BorderLayout;
 import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 import java.net.URL;
 import java.util.Vector;
 
@@ -45,7 +46,7 @@ public class WsPreferences extends GWsPreferences
   private boolean needWsMenuUpdate;
 
   private boolean oldJws1, oldJws2, oldIndexByHost, oldIndexByType,
-          oldEnfin;
+          oldEnfin, oldWsWarning;
 
   private void initFromPreferences()
   {
@@ -63,16 +64,34 @@ public class WsPreferences extends GWsPreferences
     updateList();
     enableEnfinServices.setSelected(oldEnfin = Cache.getDefault(
             "SHOW_ENFIN_SERVICES", true));
+    enableEnfinServices.addActionListener(updateAction);
     enableJws1Services.setSelected(oldJws1 = Cache.getDefault(
             "SHOW_JWS1_SERVICES", true));
+    enableJws1Services.addActionListener(updateAction);
     enableJws2Services.setSelected(oldJws2 = Cache.getDefault(
             "SHOW_JWS2_SERVICES", true));
+    enableJws2Services.addActionListener(updateAction);
     indexByHost.setSelected(oldIndexByHost = Cache.getDefault(
             "WSMENU_BYHOST", true));
+    indexByHost.addActionListener(updateAction);
     indexByType.setSelected(oldIndexByType = Cache.getDefault(
             "WSMENU_BYTYPE", true));
+    indexByType.addActionListener(updateAction);
+    displayWsWarning.setSelected(oldWsWarning = Cache.getDefault(
+            "SHOW_WSDISCOVERY_ERRORS", true));
   }
 
+  ActionListener updateAction = new ActionListener()
+  {
+
+    @Override
+    public void actionPerformed(ActionEvent e)
+    {
+      update++;
+    }
+
+  };
+
   private void updateList()
   {
     wsList.setListData(wsUrls);
@@ -97,6 +116,7 @@ public class WsPreferences extends GWsPreferences
     if (sel > -1)
     {
       wsUrls.removeElementAt(sel);
+      update++;
       updateList();
     }
   }
@@ -119,6 +139,7 @@ public class WsPreferences extends GWsPreferences
         int present = wsUrls.indexOf(url);
         if (present == -1)
         {
+          update++;
           wsUrls.setElementAt(url, sel);
           updateList();
         }
@@ -165,6 +186,8 @@ public class WsPreferences extends GWsPreferences
             "WSMENU_BYTYPE",
             Boolean.valueOf(old ? oldIndexByType : indexByType.isSelected())
                     .toString());
+    Cache.setProperty("SHOW_WSDISCOVERY_ERRORS",
+            Boolean.valueOf(old ? oldWsWarning : displayWsWarning.isSelected()).toString());
     updateServiceList();
   }
 
@@ -297,6 +320,7 @@ public class WsPreferences extends GWsPreferences
         {
           wsUrls.addElement(url);
         }
+        update++;
         updateList();
       }
     }
@@ -316,6 +340,8 @@ public class WsPreferences extends GWsPreferences
 
       public void run()
       {
+        // force a refresh.
+        lastrefresh = update - 1;
         updateWsMenuConfig(false);
         refreshWsMenu(true);
       }
@@ -324,6 +350,8 @@ public class WsPreferences extends GWsPreferences
   }
 
   /**
+   * Refresh the web services menus - but only if there has been a change in the
+   * configuration (indicated by update!=lastrefresh)
    * 
    * @param showProgress
    *          show progress in dialog or on desktop
@@ -340,8 +368,12 @@ public class WsPreferences extends GWsPreferences
           progressBar.setVisible(true);
           validate();
           progressBar.setIndeterminate(true);
-          Desktop.instance.startServiceDiscovery(true); // wait around for all
-                                                        // threads to complete
+          if (lastrefresh != update)
+          {
+            lastrefresh = update;
+            Desktop.instance.startServiceDiscovery(true); // wait around for all
+                                                          // threads to complete
+          }
           progressBar.setIndeterminate(false);
           progressBar.setVisible(false);
           validate();
@@ -359,15 +391,23 @@ public class WsPreferences extends GWsPreferences
           long ct = System.currentTimeMillis();
           Desktop.instance.setProgressBar("Refreshing Web Service Menus",
                   ct);
-          Desktop.instance.startServiceDiscovery(true);
-          Desktop.instance.setProgressBar(null,
-                  ct);
+          if (lastrefresh != update)
+          {
+            lastrefresh = update;
+            Desktop.instance.startServiceDiscovery(true);
+          }
+          Desktop.instance.setProgressBar(null, ct);
         }
 
       }).start();
     }
   }
 
+  /**
+   * state counters for ensuring that updates only happen if config has changed.
+   */
+  private long update = 0, lastrefresh = 0;
+
   /*
    * (non-Javadoc)
    * 

diff --git a/src/jalview/jbgui/GWsPreferences.java b/src/jalview/jbgui/GWsPreferences.java
index 2b30f47..da9322c 100644 (file)
--- a/src/jalview/jbgui/GWsPreferences.java
+++ b/src/jalview/jbgui/GWsPreferences.java
@@ -71,6 +71,8 @@ public class GWsPreferences extends JPanel
 
   protected JCheckBox enableEnfinServices = new JCheckBox();
 
+  protected JCheckBox displayWsWarning = new JCheckBox();
+
   protected JButton refreshWs = new JButton();
 
   protected JButton resetWs = new JButton();
@@ -178,6 +180,17 @@ public class GWsPreferences extends JPanel
         enableJws1Services_actionPerformed(e);
       }
     });
+    displayWsWarning.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    displayWsWarning.setText("Display warnings");
+    displayWsWarning
+            .setToolTipText("<html>Check this option if you want to be informed<br>when a web service URL cannot be accessed by Jalview<br>when it starts up");
+    displayWsWarning.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        displayWsWarning_actionPerformed(e);
+      }
+    });
     newWsUrl.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
     newWsUrl.setText("New Service URL");
     newWsUrl.addActionListener(new ActionListener()
@@ -294,6 +307,7 @@ public class GWsPreferences extends JPanel
     wsMenuButtons.add(enableJws1Services);
     wsMenuButtons.add(enableJws2Services);
     wsMenuButtons.add(enableEnfinServices);
+    wsMenuButtons.add(displayWsWarning);
     wsMenuRefreshButs.setLayout(new FlowLayout());
     wsMenuRefreshButs.setPreferredSize(new Dimension(480, 30));
     wsMenuRefreshButs.setSize(new Dimension(480, 30));
@@ -306,6 +320,12 @@ public class GWsPreferences extends JPanel
     add(wsMenuRefreshButs, BorderLayout.SOUTH);
   }
 
+  protected void displayWsWarning_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
   protected void resetWs_actionPerformed(ActionEvent e)
   {