X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FEmblXmlSource.java;h=73e67aa2ea377c7a912ee4885174cf685cea5ac6;hb=30b2b47cbdfa35b127b0fb09e911815cddd9ed7b;hp=008522136f00a787cda134b3f3e0cfad4ea7c3ac;hpb=9fe87bd08ab29b6fe53364f387d7a2e3a8d39994;p=jalview.git

diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index 0085221..73e67aa 100644
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -63,7 +63,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     try
     {
       reply = dbFetch.fetchDataAsFile(
-              emprefx.toLowerCase() + ":" + query.trim(), "emblxml", null,
+              emprefx.toLowerCase() + ":" + query.trim(), "display=xml",
               ".xml");
     } catch (Exception e)
     {
@@ -72,7 +72,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
               "exception.ebiembl_retrieval_failed_on", new String[] {
                   emprefx.toLowerCase(), query.trim() }), e);
     }
-    return getEmblSequenceRecords(emprefx, query, reply);
+    return getEmblSequenceRecords(emprefx, reply);
   }
 
   /**
@@ -81,46 +81,38 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
    * @param emprefx
    *          either EMBL or EMBLCDS strings are allowed - anything else will
    *          not retrieve emblxml
-   * @param query
    * @param file
    *          the EMBL XML file containing the results of a query
    * @return
    * @throws Exception
    */
-  public AlignmentI getEmblSequenceRecords(String emprefx, String query,
-          File reply) throws Exception
+  public AlignmentI getEmblSequenceRecords(String emprefx, File reply)
+          throws Exception
   {
-    EmblFile efile = null;
-    List<SequenceI> seqs = new ArrayList<SequenceI>();
+    EmblEntry entry = null;
 
     if (reply != null && reply.exists())
     {
       file = reply.getAbsolutePath();
       if (reply.length() > EMBL_NOT_FOUND_REPLY.length())
       {
-        efile = EmblFile.getEmblFile(reply);
+        entry = EmblFile.getEmblEntry(reply);
       }
     }
 
+    // TODO don't need peptides any more?
     List<SequenceI> peptides = new ArrayList<SequenceI>();
-    if (efile != null)
+    AlignmentI al = null;
+    if (entry != null)
     {
-      for (EmblEntry entry : efile.getEntries())
+      SequenceI seq = entry.getSequence(emprefx, peptides);
+      if (seq != null)
       {
-        SequenceI seq = entry.getSequence(emprefx, peptides);
-        if (seq != null)
-        {
-          seqs.add(seq.deriveSequence());
-          // place DBReferences on dataset and refer
-        }
+        seq.deriveSequence();
+        // place DBReferences on dataset and refer
+        al = new Alignment(new SequenceI[] { seq });
       }
     }
-
-    AlignmentI al = null;
-    if (!seqs.isEmpty())
-    {
-      al = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
-    }
     stopQuery();
     return al;
   }