resolve conflict with Mungo's merge

diff --combined src/jalview/ws/dbsources/EmblXmlSource.java
index d063247,4041606..0085221
--- 1/src/jalview/ws/dbsources/EmblXmlSource.java
--- 2/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@@ -29,14 -29,15 +29,15 @@@ import jalview.util.MessageManager
  import jalview.ws.ebi.EBIFetchClient;
  
  import java.io.File;
+ import java.util.ArrayList;
+ import java.util.List;
  
  public abstract class EmblXmlSource extends EbiFileRetrievedProxy
  {
- 
-   /**
-    * Last properly parsed embl file.
+   /*
+    * JAL-1856 Embl returns this text for query not found
     */
-   public EmblFile efile = null;
+   private static final String EMBL_NOT_FOUND_REPLY = "ERROR 12 No entries found.";
  
    public EmblXmlSource()
    {
@@@ -62,8 -63,7 +63,8 @@@
      try
      {
        reply = dbFetch.fetchDataAsFile(
 -              emprefx.toLowerCase() + ":" + query.trim(), "emblxml", null);
 +              emprefx.toLowerCase() + ":" + query.trim(), "emblxml", null,
 +              ".xml");
      } catch (Exception e)
      {
        stopQuery();
@@@ -89,68 -89,36 +90,36 @@@
    public AlignmentI getEmblSequenceRecords(String emprefx, String query,
            File reply) throws Exception
    {
-     SequenceI seqs[] = null;
-     StringBuffer result = new StringBuffer();
+     EmblFile efile = null;
+     List<SequenceI> seqs = new ArrayList<SequenceI>();
+ 
      if (reply != null && reply.exists())
      {
-       efile = null;
        file = reply.getAbsolutePath();
-       if (reply.length() > 25)
+       if (reply.length() > EMBL_NOT_FOUND_REPLY.length())
        {
          efile = EmblFile.getEmblFile(reply);
        }
-       else
-       {
-         result.append(MessageManager.formatMessage(
-                 "label.no_embl_record_found",
-                 new String[] { emprefx.toLowerCase(), query.trim() }));
-       }
      }
+ 
+     List<SequenceI> peptides = new ArrayList<SequenceI>();
      if (efile != null)
      {
        for (EmblEntry entry : efile.getEntries())
        {
-         SequenceI[] seqparts = entry.getSequences(false, true, emprefx);
-         // TODO: use !fetchNa,!fetchPeptide here instead - see todo in EmblEntry
-         if (seqparts != null)
+         SequenceI seq = entry.getSequence(emprefx, peptides);
+         if (seq != null)
          {
-           SequenceI[] newseqs = null;
-           int si = 0;
-           if (seqs == null)
-           {
-             newseqs = new SequenceI[seqparts.length];
-           }
-           else
-           {
-             newseqs = new SequenceI[seqs.length + seqparts.length];
- 
-             for (; si < seqs.length; si++)
-             {
-               newseqs[si] = seqs[si];
-               seqs[si] = null;
-             }
-           }
-           for (int j = 0; j < seqparts.length; si++, j++)
-           {
-             newseqs[si] = seqparts[j].deriveSequence();
-             // place DBReferences on dataset and refer
-           }
-           seqs = newseqs;
- 
+           seqs.add(seq.deriveSequence());
+           // place DBReferences on dataset and refer
          }
        }
      }
-     else
-     {
-       result = null;
-     }
+ 
      AlignmentI al = null;
-     if (seqs != null && seqs.length > 0)
+     if (!seqs.isEmpty())
      {
-       al = new Alignment(seqs);
-       result.append(MessageManager.formatMessage(
-               "label.embl_successfully_parsed", new String[] { emprefx }));
-       results = result;
+       al = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
      }
      stopQuery();
      return al;

diff --combined src/jalview/ws/ebi/EBIFetchClient.java
index 468b7f0,b09cbaa..9f6bc65
--- 1/src/jalview/ws/ebi/EBIFetchClient.java
--- 2/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@@ -20,6 -20,7 +20,7 @@@
   */
  package jalview.ws.ebi;
  
+ import jalview.datamodel.DBRefSource;
  import jalview.util.MessageManager;
  
  import java.io.BufferedInputStream;
@@@ -90,22 -91,22 +91,24 @@@ public class EBIFetchClien
     * 
     * @param ids
     *          the query formatted as db:query1;query2;query3
-    * @param f
+    * @param format
     *          the format wanted
     * @param s
     *          - unused parameter
     * @return the file holding the response
     * @throws OutOfMemoryError
     */
-   public File fetchDataAsFile(String ids, String f, String s, String ext)
 -  public File fetchDataAsFile(String ids, String format, String s)
++
++  public File fetchDataAsFile(String ids, String format, String s,
++          String ext)
            throws OutOfMemoryError
    {
      File outFile = null;
      try
      {
 -      outFile = File.createTempFile("jalview", ".xml");
 +      outFile = File.createTempFile("jalview", ext);
        outFile.deleteOnExit();
-       fetchData(ids, f, s, outFile);
+       fetchData(ids, format, s, outFile);
        if (outFile.length() == 0)
        {
          outFile.delete();
@@@ -122,20 -123,20 +125,20 @@@
     * 
     * @param ids
     *          db:query1;query2;query3
-    * @param f
+    * @param format
     *          raw/xml
     * @param s
     *          not used - remove?
     * 
     * @return Raw string array result of query set
     */
-   public String[] fetchData(String ids, String f, String s)
+   public String[] fetchData(String ids, String format, String s)
            throws OutOfMemoryError
    {
-     return fetchData(ids, f, s, null);
+     return fetchData(ids, format, s, null);
    }
  
-   public String[] fetchData(String ids, String f, String s, File outFile)
+   String[] fetchData(String ids, String f, String s, File outFile)
            throws OutOfMemoryError
    {
      // Need to split
@@@ -183,16 -184,27 +186,27 @@@
      return (rslts.length == 0 ? null : rslts);
    }
  
-   public String[] fetchBatch(String ids, String db, String f, String s,
+   public String[] fetchBatch(String ids, String dbPath, String format, String s,
            File outFile) throws OutOfMemoryError
    {
-     long time = System.currentTimeMillis();
-     // max 200 ids can be added at one time
+     // long time = System.currentTimeMillis();
+     /*
+      * JAL-1855 dbfetch from ena_sequence, ena_coding
+      */
+     if (dbPath.equalsIgnoreCase(DBRefSource.EMBL))
+     {
+       dbPath = "ena_sequence";
+     }
+     else if (dbPath.equalsIgnoreCase(DBRefSource.EMBLCDS))
+     {
+       dbPath = "ena_coding";
+     }
+ 
      try
      {
        URL rcall = new URL("http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
-               + db.toLowerCase() + "/" + ids.toLowerCase()
-               + (f != null ? "/" + f : ""));
+               + dbPath.toLowerCase() + "/" + ids.toLowerCase()
+               + (format != null ? "/" + format : ""));
  
        InputStream is = new BufferedInputStream(rcall.openStream());
        if (outFile != null)
@@@ -221,7 -233,7 +235,7 @@@
      } catch (OutOfMemoryError er)
      {
  
-       System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + db
+       System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + dbPath
                + ":\n" + ids);
        throw er;
      } catch (Exception ex)
@@@ -231,14 -243,15 +245,15 @@@
        {
          return null;
        }
-       System.err.println("Unexpected exception when retrieving from " + db
+       System.err.println("Unexpected exception when retrieving from "
+               + dbPath
                + "\nQuery was : '" + ids + "'");
        ex.printStackTrace(System.err);
        return null;
      } finally
      {
-       // System.err.println("Took " + (System.currentTimeMillis() - time)
-       // / 1000 + " secs for one call.");
+       // System.err.println("EBIFetch took " + (System.currentTimeMillis() -
+       // time) + " ms");
      }
      return null;
    }