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 06e929d..4d09bdc 100644 (file)
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -48,8 +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/ena/data/view/J03321&display=xml
+ * For example: http://www.ebi.ac.uk/ena/data/view/J03321&display=xml
  * 
  * @see embl_mapping.xml
  */
@@ -195,13 +194,11 @@ public class EmblEntry
     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
      */
@@ -299,7 +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"))
         {
@@ -470,13 +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)
             {
@@ -504,7 +503,6 @@ public class EmblEntry
             dnaToProteinMapping.setTo(proteinSeq);
             dnaToProteinMapping.setMappedFromId(proteinId);
             proteinSeq.addDBRef(proteinDbRef);
-            proteinSeq.setSourceDBRef(proteinDbRef);
             ref.setMap(dnaToProteinMapping);
           }
           hasUniprotDbref = true;
@@ -549,7 +547,6 @@ public class EmblEntry
                 DBRefSource.EMBLCDSProduct, getSequenceVersion(), proteinId);
       }
       product.addDBRef(proteinToEmblProteinRef);
-      product.setSourceDBRef(proteinToEmblProteinRef);
 
       if (dnaToProteinMapping != null
               && dnaToProteinMapping.getTo() != null)