X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=5ce7d285c4c93f81473e4cc6df4770b00871c12e;hb=28932bb93da81aff277d509d9a624a1119a4a979;hp=76e73e4a827e27d65a797cfaf5098ea47178d7ac;hpb=2253f31565d4e96edffce2fac596e2ef0578d596;p=jalview.git

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 76e73e4..5ce7d28 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.0.b2)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -213,27 +213,30 @@ public class DBRefFetcher implements Runnable
         {
           // Still queries to make for current seqIndex
           StringBuffer queryString = new StringBuffer("");
-          int nqSize = (maxqlen > queries.size()) ? queries.size()
+          int numq=0,nqSize = (maxqlen > queries.size()) ? queries.size()
                   : maxqlen;
-          for (int nq = 0, numq = 0; nq < nqSize; nq++)
+          
+          while (queries.size()>0 && numq < nqSize)
           {
-            String query = (String) queries.elementAt(nq);
+            String query = (String) queries.elementAt(0);
             if (dbsource.isValidReference(query))
             {
-              queryString.append((nq == 0) ? "" : dbsource
+              queryString.append((numq == 0) ? "" : dbsource
                       .getAccessionSeparator());
               queryString.append(query);
               numq++;
             }
-          }
-          for (int nq = 0; nq < nqSize; nq++)
-          {
+            // remove the extracted query string
             queries.removeElementAt(0);
           }
           // make the queries and process the response
           AlignmentI retrieved = null;
           try
           {
+            if (jalview.bin.Cache.log.isDebugEnabled())
+            {
+              jalview.bin.Cache.log.debug("Querying "+dbsource.getDbName()+" with : '"+queryString.toString()+"'");
+            }
             retrieved = dbsource.getSequenceRecords(queryString.toString());
           } catch (Exception ex)
           {
@@ -259,7 +262,7 @@ public class DBRefFetcher implements Runnable
                     { dbSources[db] }); // jalview.datamodel.DBRefSource.UNIPROT
             // });
             // check for existing dbrefs to use
-            if (uprefs != null)
+            if (uprefs != null && uprefs.length>0)
             {
               for (int j = 0; j < uprefs.length; j++)
               {