From dc734ef1e078af1a0329000fb6839e2e08b7e16b Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 11 Mar 2010 17:18:40 +0000
Subject: [PATCH] warning for unresolvable database source strings (or ones
 which apparently have no cross references)

---
 src/jalview/ws/DBRefFetcher.java |   32 ++++++++++++++++++--------------
 1 file changed, 18 insertions(+), 14 deletions(-)

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 73d106a..581901a 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -500,27 +500,31 @@ public class DBRefFetcher implements Runnable
       DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(entry
               .getDBRef(), new String[]
       { dbSource });
+      if (entryRefs==null) {
+        System.err.println("Dud dbSource string ? no entryrefs selected for "+dbSource+ " on "+entry.getName());
+        continue;
+      }
       for (int j = 0; j < entryRefs.length; j++)
-      {
-        String accessionId = entryRefs[j].getAccessionId(); // .getAccession().elementAt(j).toString();
-        // match up on accessionId
-        if (seqRefs.containsKey(accessionId.toUpperCase()))
         {
-          Vector seqs = (Vector) seqRefs.get(accessionId);
-          for (int jj = 0; jj < seqs.size(); jj++)
+          String accessionId = entryRefs[j].getAccessionId(); // .getAccession().elementAt(j).toString();
+          // match up on accessionId
+          if (seqRefs.containsKey(accessionId.toUpperCase()))
           {
-            sequence = (SequenceI) seqs.elementAt(jj);
-            if (!sequenceMatches.contains(sequence))
+            Vector seqs = (Vector) seqRefs.get(accessionId);
+            for (int jj = 0; jj < seqs.size(); jj++)
             {
-              sequenceMatches.addElement(sequence);
+              sequence = (SequenceI) seqs.elementAt(jj);
+              if (!sequenceMatches.contains(sequence))
+              {
+                sequenceMatches.addElement(sequence);
+              }
             }
           }
         }
-      }
-      if (sequenceMatches.size() == 0)
-      {
-        // failed to match directly on accessionId==query so just compare all
-        // sequences to entry
+        if (sequenceMatches.size() == 0)
+        {
+          // failed to match directly on accessionId==query so just compare all
+          // sequences to entry
         Enumeration e = seqRefs.keys();
         while (e.hasMoreElements())
         {
-- 
1.7.10.2