X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FEmblXmlSource.java;h=66ebe1bedb298dedd9363b8e8ee36ca4369c7e62;hb=c6c67aaa8e2d236305a3495f4edfc8cc88e22b79;hp=58ee42dc83f82dfadcb430a6c98ef337be53d9e7;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index 58ee42d..66ebe1b 100644
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -24,11 +24,11 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.xdb.embl.EmblEntry;
+import jalview.datamodel.xdb.embl.EmblFile;
 import jalview.util.MessageManager;
 import jalview.ws.ebi.EBIFetchClient;
 
 import java.io.File;
-import java.util.Iterator;
 
 public abstract class EmblXmlSource extends EbiFileRetrievedProxy
 {
@@ -36,7 +36,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
   /**
    * Last properly parsed embl file.
    */
-  public jalview.datamodel.xdb.embl.EmblFile efile = null;
+  public EmblFile efile = null;
 
   public EmblXmlSource()
   {
@@ -66,7 +66,9 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     } catch (Exception e)
     {
       stopQuery();
-      throw new Exception(MessageManager.formatMessage("exception.ebiembl_retrieval_failed_on", new String[]{emprefx.toLowerCase(),query.trim()}), e);
+      throw new Exception(MessageManager.formatMessage(
+              "exception.ebiembl_retrieval_failed_on", new String[] {
+                  emprefx.toLowerCase(), query.trim() }), e);
     }
     return getEmblSequenceRecords(emprefx, query, reply);
   }
@@ -94,28 +96,21 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
       file = reply.getAbsolutePath();
       if (reply.length() > 25)
       {
-        efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);
+        efile = EmblFile.getEmblFile(reply);
       }
       else
       {
-        result.append(MessageManager.formatMessage("label.no_embl_record_found", new String[]{emprefx.toLowerCase(),query.trim()}));
+        result.append(MessageManager.formatMessage(
+                "label.no_embl_record_found",
+                new String[] { emprefx.toLowerCase(), query.trim() }));
       }
     }
     if (efile != null)
     {
-      for (Iterator i = efile.getEntries().iterator(); i.hasNext();)
+      for (EmblEntry entry : efile.getEntries())
       {
-        EmblEntry entry = (EmblEntry) i.next();
-        SequenceI[] seqparts = entry.getSequences(false, true, emprefx); // TODO:
-        // use
-        // !fetchNa,!fetchPeptide
-        // here
-        // instead
-        // -
-        // see
-        // todo
-        // in
-        // emblEntry
+        SequenceI[] seqparts = entry.getSequences(false, true, emprefx);
+        // TODO: use !fetchNa,!fetchPeptide here instead - see todo in EmblEntry
         if (seqparts != null)
         {
           SequenceI[] newseqs = null;
@@ -136,8 +131,8 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
           }
           for (int j = 0; j < seqparts.length; si++, j++)
           {
-            newseqs[si] = seqparts[j].deriveSequence(); // place DBReferences on
-            // dataset and refer
+            newseqs[si] = seqparts[j].deriveSequence();
+            // place DBReferences on dataset and refer
           }
           seqs = newseqs;
 
@@ -152,11 +147,18 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     if (seqs != null && seqs.length > 0)
     {
       al = new Alignment(seqs);
-      result.append(MessageManager.formatMessage("label.embl_successfully_parsed", new String[]{emprefx}));
+      result.append(MessageManager.formatMessage(
+              "label.embl_successfully_parsed", new String[] { emprefx }));
       results = result;
     }
     stopQuery();
     return al;
   }
 
+  @Override
+  public boolean isDnaCoding()
+  {
+    return true;
+  }
+
 }