From 4944c2f33bb34b4f262fd2f3ae40dcdc2a825557 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 13 Mar 2006 16:52:54 +0000
Subject: [PATCH] fixes bug 0013013 but reveals lack of a 'features retrieved'
 flag that should be set when a sequence's uniprot record
 has been retrieved and all its sequence features have been
 added.

---
 src/jalview/io/SequenceFeatureFetcher.java |   18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/src/jalview/io/SequenceFeatureFetcher.java b/src/jalview/io/SequenceFeatureFetcher.java
index 7f11149..00afc39 100755
--- a/src/jalview/io/SequenceFeatureFetcher.java
+++ b/src/jalview/io/SequenceFeatureFetcher.java
@@ -113,8 +113,14 @@ public class SequenceFeatureFetcher implements Runnable
              seqIndex++, i++)
         {
           Sequence sequence = (Sequence) sequences.get(seqIndex);
-          if(sequence.getSequenceFeatures()==null)
+          Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(), new String[] { "Uniprot"});
+          if (uprefs!=null)
           {
+            // we know the id for this entry, so don't note its ID in the unknownSequences list
+            for (int j=0,k=uprefs.size(); j<k; j++)
+              ids.add(((DBRefEntry) uprefs.get(j)).getAccessionId());
+            unknownSequences.add(sequence);
+          } else {
             if (!ids.contains(sequence.getName()))
             {
               ids.add(sequence.getName());
@@ -301,10 +307,12 @@ public class SequenceFeatureFetcher implements Runnable
       }
 
       sequence.setPDBId(onlyPdbEntries);
-      e = entry.getFeature().elements();
-      while(e.hasMoreElements())
-      {
-          sequence.addSequenceFeature((SequenceFeature)e.nextElement());
+      if (entry.getFeature()!=null) {
+        e = entry.getFeature().elements();
+        while (e.hasMoreElements())
+        {
+          sequence.addSequenceFeature( (SequenceFeature) e.nextElement());
+        }
       }
       sequence.setStart(absStart);
       sequence.setEnd(absEnd);
-- 
1.7.10.2