first stage of adapting JNet client to hidden regions and new WSClient

[jalview.git] / src / jalview / ws / Discoverer.java

diff --git a/src/jalview/ws/Discoverer.java b/src/jalview/ws/Discoverer.java
index 4921fb7..bf08dcd 100755 (executable)
--- a/src/jalview/ws/Discoverer.java
+++ b/src/jalview/ws/Discoverer.java
@@ -34,6 +34,7 @@ import ext.vamsas.*;
 import java.util.Vector;
 import java.util.Hashtable;
 import java.util.StringTokenizer;
+import javax.swing.JOptionPane;
 
 public class Discoverer
     extends Thread implements Runnable
@@ -144,9 +145,13 @@ public class Discoverer
       return urls;
     return null;
   }
-  static
-  {
 
+  /**
+   * fetch new services or reset to hardwired defaults depending on preferences.
+   */
+  static public void doDiscovery()
+  {
+    jalview.bin.Cache.log.debug("(Re)-Initialising the discovery URL list.");
     try
     {
       reallyDiscoverServices = jalview.bin.Cache.getDefault("DISCOVERY_START", false);
@@ -169,6 +174,13 @@ public class Discoverer
 ),
             new ServiceHandle(
                 "MsaWS",
+                "Katoh, K., K. Kuma, K., Toh, H.,  and Miyata, T. (2005) "+
+                "\"MAFFT version 5: improvement in accuracy of multiple sequence alignment.\""+
+               " Nucleic Acids Research, 33 511-518",
+                "http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS",
+                "MAFFT Multiple Sequence Alignment"),
+            new ServiceHandle(
+                "MsaWS",
                 "Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple" +
                 " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice." +
                 " Nucleic Acids Research, 22 4673-4680",
@@ -176,7 +188,7 @@ public class Discoverer
                 "ClustalW Multiple Sequence Alignment"),
             new ServiceHandle(
                 "SecStrPred",
-                "Cuff J. A and Barton G.J (1999) Application of enhanced " +
+                "Cuff J. A and Barton G.J (2000) Application of " +
                 "multiple sequence alignment profiles to improve protein secondary structure prediction, " +
                 "Proteins 40:502-511",
                 "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred","JNet Secondary Structure Prediction"
@@ -206,12 +218,23 @@ public class Discoverer
       jalview.bin.Cache.log.debug("Discovering services using " + location);
       shs = locateWebService(location).getServices();
     }
-    catch (Exception e)
-    {
-      jalview.bin.Cache.log.debug("No Discovery service at " +
-                         location);
-      jalview.bin.Cache.log.debug(e);
-
+    catch (org.apache.axis.AxisFault f) {
+      // JBPNote - should do this a better way!
+      if (f.getFaultReason().indexOf("(407)")>-1) {
+        if (jalview.gui.Desktop.desktop!=null)
+          JOptionPane.showMessageDialog(jalview.gui.Desktop.desktop, "Please set up your proxy settings in the 'Connections' tab of the Preferences window",
+                                      "Proxy Authorization Failed",
+                                      JOptionPane.WARNING_MESSAGE);
+      } else {
+        jalview.bin.Cache.log.warn("No Discovery service at " +
+                                   location);
+        jalview.bin.Cache.log.debug("Axis Fault", f);
+      }
+    }
+    catch (Exception e) {
+      jalview.bin.Cache.log.warn("No Discovery service at " +
+                                 location);
+      jalview.bin.Cache.log.debug("Discovery Service General Exception", e);
     }
     if ( (shs != null) && shs.getServices().length > 0)
     {
@@ -314,8 +337,18 @@ public class Discoverer
     firePropertyChange("services", oldServices, services);
   }
 
+  /**
+   * creates a new thread to call discoverServices()
+   */
   public void run()
   {
-    discoverServices();
+    final Discoverer discoverer = this;
+    Thread discoverThread = new Thread() {
+      public void run() {
+        discoverer.doDiscovery();
+        discoverer.discoverServices();
+      }
+    };
+    discoverThread.start();
   }
 }