quick fix for exceptions due to invalid embl refs

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 10e1b59..2f92333 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -228,10 +228,10 @@ extends JPanel implements Runnable
       while(st.hasMoreTokens())
       {
         EBIFetchClient dbFetch = new EBIFetchClient();
-
+        String qry = database.getSelectedItem().toString().toLowerCase(
+        ) + ":" + st.nextToken();
         File reply = dbFetch.fetchDataAsFile(
-            database.getSelectedItem().toString().toLowerCase(
-            ) + ":" + st.nextToken(),
+            qry,
             "emblxml",null);
 
         jalview.datamodel.xdb.embl.EmblFile efile=null;
@@ -264,12 +264,14 @@ extends JPanel implements Runnable
             }
           }
         } else {
-          result=null;
+          result.append("# no response for "+qry);
         }
       }
       if (seqs!=null && seqs.length>0) {
         if (parseResult(new Alignment(seqs), null, null)!=null)
-          result.append("# Successfully parsed the "+database.getSelectedItem()+" Queries into an Alignment");
+        {
+            result.append("# Successfully parsed the "+database.getSelectedItem()+" Queries into an Alignment");
+        }
       }
     }
     else if (database.getSelectedItem().equals("PDB"))