X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fseqfetcher%2FASequenceFetcher.java;h=4d182cd4c4766f6166ae670578f274b9d2e1221c;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=f449570e91c99c2d7bff0e8bdfb270afdbfd6bde;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
index f449570..4d182cd 100644
--- a/src/jalview/ws/seqfetcher/ASequenceFetcher.java
+++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ws.seqfetcher;
 
@@ -21,9 +24,9 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceI;
 import jalview.util.DBRefUtils;
+import jalview.util.MessageManager;
 
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.Enumeration;
 import java.util.HashSet;
 import java.util.Hashtable;
@@ -273,9 +276,11 @@ public class ASequenceFetcher
       DbSourceProxy[] l = dblist.values().toArray(new DbSourceProxy[0]);
       int i = 0;
       String[] nm = new String[l.length];
+      // make sure standard dbs appear first, followed by reference das sources,
+      // followed by anything else.
       for (DbSourceProxy s : l)
       {
-        nm[i++] = s.getDbName().toLowerCase();
+        nm[i++] = "" + s.getTier() + s.getDbName().toLowerCase();
       }
       jalview.util.QuickSort.sort(nm, l);
       dbs = new ArrayList<DbSourceProxy>();
@@ -322,7 +327,7 @@ public class ASequenceFetcher
     } catch (Exception e)
     {
       // Serious problems if this happens.
-      throw new Error("DBRefSource Implementation Exception", e);
+      throw new Error(MessageManager.getString("error.dbrefsource_implementation_exception"), e);
     }
     addDbRefSourceImpl(proxy);
   }
@@ -390,9 +395,7 @@ public class ASequenceFetcher
   {
     if (!jalview.ws.seqfetcher.DbSourceProxy.class.isAssignableFrom(class1))
     {
-      throw new Error(
-              "Implmentation Error - getDbInstances must be given a class that implements jalview.ws.seqfetcher.DbSourceProxy (was given '"
-                      + class1 + "')");
+      throw new Error(MessageManager.formatMessage("error.implementation_error_dbinstance_must_implement_interface", new String[]{class1.toString()}));
     }
     if (FETCHABLEDBS == null)
     {