X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceFeatureFetcher.java;h=61b25f932b70ed01b65d03ddc7dbc53b3e7a218d;hb=b01c4edc00dbeedd6b53777310d4232a4104a9ec;hp=3e74da56f4ab4dfded682f45934b7eaa9e5062d4;hpb=216dc75e0d19834edbfb84a89e6e33354cea6025;p=jalview.git

diff --git a/src/jalview/io/SequenceFeatureFetcher.java b/src/jalview/io/SequenceFeatureFetcher.java
index 3e74da5..61b25f9 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());
@@ -187,7 +193,7 @@ public class SequenceFeatureFetcher implements Runnable
         //             javax.swing.JOptionPane.YES_NO_OPTION, javax.swing.JOptionPane.QUESTION_MESSAGE);
      javax.swing.JOptionPane.showMessageDialog(
     Desktop.desktop, "Couldn't find a match for "+unknownSequences.size()+" sequences.",
-            "Blast for Unidentified Sequences",
+            "Unidentified Sequences",
              javax.swing.JOptionPane.WARNING_MESSAGE);
 
 
@@ -301,7 +307,15 @@ public class SequenceFeatureFetcher implements Runnable
       }
 
       sequence.setPDBId(onlyPdbEntries);
-      sequence.setSequenceFeatures(entry.getFeature());
+      if (entry.getFeature()!=null) {
+        e = entry.getFeature().elements();
+        while (e.hasMoreElements())
+        {
+          SequenceFeature sf = (SequenceFeature) e.nextElement();
+          sf.setFeatureGroup("Uniprot");
+          sequence.addSequenceFeature( sf );
+        }
+      }
       sequence.setStart(absStart);
       sequence.setEnd(absEnd);