cleaned up some comments and exception messages.

diff --git a/src/ext/jemboss/soap/PrivateRequest.java b/src/ext/jemboss/soap/PrivateRequest.java
index 582949d..892db3a 100755 (executable)
--- a/src/ext/jemboss/soap/PrivateRequest.java
+++ b/src/ext/jemboss/soap/PrivateRequest.java
@@ -174,8 +174,7 @@ public class PrivateRequest
            if(msg.startsWith("Failed Authorisation"))
              throw new JembossSoapException("Authentication Failed");
            else if(msg.startsWith("Error"))
-             JOptionPane.showMessageDialog(null, msg, "alert",
-                                   JOptionPane.ERROR_MESSAGE);
+             throw new JembossSoapException(msg);
          }
          proganswer.put(s,vans.get(j+1));
        }
@@ -183,8 +182,10 @@ public class PrivateRequest
      catch (Exception e)
      {
         System.out.println("Exception in PrivateRequest "+
-                            e.getMessage ());
-        throw new JembossSoapException("  Fault Code   = " );
+                            e.getMessage ()
+                           );
+        e.printStackTrace();
+        throw new JembossSoapException("  Fault Code   = " + e);
      }
 
    }

diff --git a/src/jalview/ws/Jemboss.java b/src/jalview/ws/Jemboss.java
index 7c107c7..336be27 100755 (executable)
--- a/src/jalview/ws/Jemboss.java
+++ b/src/jalview/ws/Jemboss.java
@@ -20,9 +20,10 @@ package jalview.ws;
  * functionality.
  *
  * Things to do
- * Test threadability
  * Standardise the exceptions (currently errors are output on stdout)
  * Allow server configuration
+ * Throw away JembossParams and Jemboss dependence
+ * Generalise results to return collections of objects - alignments, trees, annotations, etc.
  */
 
 import java.net.*;
@@ -162,7 +163,7 @@ public class Jemboss
           String alfile = h.get(thiskey).toString();
           String format = IdentifyFile.Identify(alfile, "Paste");
           SequenceI[] alignment = null;
-
+          
           if (FormatProperties.contains(format))
             alignment = FormatAdapter.read(alfile, "Paste", format);
           else