X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Fxdb%2Fembl%2FEmblEntry.java;h=4d09bdc2a408d74ba04ec1e61ae48482f00bd0fb;hb=a25f31a9140c9764baf76ec1c2ede98c1e3e52f9;hp=56b132508ce5ad76c91fef93ce9885864fb02443;hpb=c14d9e8c9ff59de1857d4834ee70e80abf623415;p=jalview.git

diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index 56b1325..4d09bdc 100644
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -48,9 +48,7 @@ import java.util.regex.Pattern;
  * Data model for one entry returned from an EMBL query, as marshalled by a
  * Castor binding file
  * 
- * For example:
- * http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=ena_sequence&id=J03321
- * &format=emblxml
+ * For example: http://www.ebi.ac.uk/ena/data/view/J03321&display=xml
  * 
  * @see embl_mapping.xml
  */
@@ -188,17 +186,19 @@ public class EmblEntry
   public SequenceI getSequence(String sourceDb, List<SequenceI> peptides)
   {
     SequenceI dna = makeSequence(sourceDb);
+    if (dna == null)
+    {
+      return null;
+    }
     dna.setDescription(description);
     DBRefEntry retrievedref = new DBRefEntry(sourceDb,
             getSequenceVersion(), accession);
     dna.addDBRef(retrievedref);
-    dna.setSourceDBRef(retrievedref);
     // add map to indicate the sequence is a valid coordinate frame for the
     // dbref
     retrievedref.setMap(new Mapping(null, new int[] { 1, dna.getLength() },
             new int[] { 1, dna.getLength() }, 1, 1));
 
-
     /*
      * transform EMBL Database refs to canonical form
      */
@@ -240,6 +240,12 @@ public class EmblEntry
    */
   SequenceI makeSequence(String sourceDb)
   {
+    if (sequence == null)
+    {
+      System.err.println("No sequence was returned for ENA accession "
+              + accession);
+      return null;
+    }
     SequenceI dna = new Sequence(sourceDb + "|" + accession,
             sequence.getSequence());
     return dna;
@@ -290,7 +296,8 @@ public class EmblEntry
         if (qname.equals("translation"))
         {
           // remove all spaces (precompiled String.replaceAll(" ", ""))
-          translation = SPACE_PATTERN.matcher(q.getValues()[0]).replaceAll("");
+          translation = SPACE_PATTERN.matcher(q.getValues()[0]).replaceAll(
+                  "");
         }
         else if (qname.equals("protein_id"))
         {
@@ -461,13 +468,14 @@ public class EmblEntry
          */
         String source = DBRefUtils.getCanonicalName(ref.getSource());
         ref.setSource(source);
-        DBRefEntry proteinDbRef = new DBRefEntry(ref.getSource(), ref.getVersion(), ref
-                .getAccessionId());
+        DBRefEntry proteinDbRef = new DBRefEntry(ref.getSource(),
+                ref.getVersion(), ref.getAccessionId());
         if (source.equals(DBRefSource.UNIPROT))
         {
           String proteinSeqName = DBRefSource.UNIPROT + "|"
                   + ref.getAccessionId();
-          if (dnaToProteinMapping != null && dnaToProteinMapping.getTo() != null)
+          if (dnaToProteinMapping != null
+                  && dnaToProteinMapping.getTo() != null)
           {
             if (mappingUsed)
             {
@@ -495,7 +503,6 @@ public class EmblEntry
             dnaToProteinMapping.setTo(proteinSeq);
             dnaToProteinMapping.setMappedFromId(proteinId);
             proteinSeq.addDBRef(proteinDbRef);
-            proteinSeq.setSourceDBRef(proteinDbRef);
             ref.setMap(dnaToProteinMapping);
           }
           hasUniprotDbref = true;
@@ -540,7 +547,6 @@ public class EmblEntry
                 DBRefSource.EMBLCDSProduct, getSequenceVersion(), proteinId);
       }
       product.addDBRef(proteinToEmblProteinRef);
-      product.setSourceDBRef(proteinToEmblProteinRef);
 
       if (dnaToProteinMapping != null
               && dnaToProteinMapping.getTo() != null)