JAL-2089 patch broken merge to master for Release 2.10.0b1

[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 8688720..4d09bdc 100644 (file)
--- 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
  */
@@ -188,6 +186,10 @@ 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);
@@ -197,7 +199,6 @@ public class EmblEntry
     retrievedref.setMap(new Mapping(null, new int[] { 1, dna.getLength() },
             new int[] { 1, dna.getLength() }, 1, 1));
 
-
     /*
      * transform EMBL Database refs to canonical form
      */
@@ -239,6 +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;
@@ -289,7 +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"))
         {
@@ -460,13 +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)
             {