Merge branch 'develop' into merge/develop_bug/JAL-2154projectMappings

[jalview.git] / src / jalview / datamodel / xdb / embl / EmblEntry.java

diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index 56b1325..3ba36ca 100644 (file)
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -49,8 +49,7 @@ import java.util.regex.Pattern;
  * Castor binding file
  * 
  * For example:
- * http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=ena_sequence&id=J03321
- * &format=emblxml
+ * http://www.ebi.ac.uk/ena/data/view/J03321&display=xml
  * 
  * @see embl_mapping.xml
  */
@@ -188,11 +187,14 @@ 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() },
@@ -240,6 +242,12 @@ 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;
@@ -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)