From 9f74164360b38c5e08c89f8e687dac01ddfc98bb Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 4 Nov 2008 13:31:18 +0000
Subject: [PATCH] bugfix db ref retrieve routine so it removes dead query
 strings properly

---
 src/jalview/ws/DBRefFetcher.java |   19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 76e73e4..96ac7e8 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -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++)
               {
-- 
1.7.10.2