X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FEmblXmlSource.java;h=3179110cb124393998b7a6db5182b5c721a45d07;hb=6ebb5015f90d293322fb3af0c7b20313359fe97d;hp=1300c65f53eba77a996a371dee9dd424437778df;hpb=5d88ae6bbf1ea113cefcb43b7918b5baf560a76e;p=jalview.git

diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index 1300c65..3179110 100644
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -23,10 +23,6 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     super();
   }
   /**
-   * set this to false to *not* add protein products to alignment dataset.
-   */
-  public boolean getProteinProducts=false;
-  /**
    * retrieve and parse an emblxml file
    * @param emprefx either EMBL or EMBLCDS strings are allowed - anything else will not retrieve emblxml
    * @param query
@@ -53,13 +49,19 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     }
     if (reply != null && reply.exists())
       {
+        efile=null;
         file = reply.getAbsolutePath();
-        efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);
+        if (reply.length()>25)
+        {
+            efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);
+        } else {
+          result.append("# No EMBL record retrieved for "+emprefx.toLowerCase()+":"+query.trim());
+        }
       }
       if (efile!=null) {
         for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) {
           EmblEntry entry = (EmblEntry) i.next();
-          SequenceI[] seqparts = entry.getSequences(false,!getProteinProducts, emprefx);
+          SequenceI[] seqparts = entry.getSequences(false, true, emprefx); // TODO: use !fetchNa,!fetchPeptide here instead - see todo in emblEntry
           if (seqparts!=null) {
             SequenceI[] newseqs = null;
             int si=0;