From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 21 Jun 2016 15:13:05 +0000 (+0100)
Subject: Merge branch 'features/JAL-2110_crossRefDuplications' into merge_JAL-2110
X-Git-Tag: Release_2_10_0~140^2~5^2~49
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0ac97c219bf88278f77306a5695e8bd9d9ca9179;p=jalview.git

Merge branch 'features/JAL-2110_crossRefDuplications' into merge_JAL-2110
---

0ac97c219bf88278f77306a5695e8bd9d9ca9179
diff --cc src/jalview/datamodel/xdb/embl/EmblEntry.java
index f8c0bbe,43581da..5409d5b
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@@ -198,6 -198,9 +198,10 @@@ public class EmblEntr
      retrievedref.setMap(new Mapping(null, new int[] { 1, dna.getLength() },
              new int[] { 1, dna.getLength() }, 1, 1));
  
++
+     /*
+      * transform EMBL Database refs to canonical form
+      */
      if (dbRefs != null)
      {
        for (DBRefEntry dbref : dbRefs)
diff --cc src/jalview/gui/Jalview2XML.java
index eeb4214,dfd2119..df076d9
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@@ -2714,12 -2697,8 +2714,12 @@@ public class Jalview2XM
      SequenceI[] orderedSeqs = tmpseqs
              .toArray(new SequenceI[tmpseqs.size()]);
  
-     Alignment al = new Alignment(orderedSeqs);
+     AlignmentI al = new Alignment(orderedSeqs);
  
 +    if (referenceseqForView != null)
 +    {
 +      al.setSeqrep(referenceseqForView);
 +    }
      // / Add the alignment properties
      for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
      {
diff --cc src/jalview/ws/jws1/SeqSearchWSThread.java
index 66fddd1,86c2b9f..70056a6
--- a/src/jalview/ws/jws1/SeqSearchWSThread.java
+++ b/src/jalview/ws/jws1/SeqSearchWSThread.java
@@@ -21,9 -21,9 +21,10 @@@
  package jalview.ws.jws1;
  
  import jalview.analysis.AlignSeq;
 +import jalview.api.FeatureColourI;
  import jalview.bin.Cache;
  import jalview.datamodel.Alignment;
+ import jalview.datamodel.AlignmentI;
  import jalview.datamodel.AlignmentView;
  import jalview.datamodel.SequenceI;
  import jalview.gui.AlignFrame;
@@@ -172,8 -172,8 +173,8 @@@ class SeqSearchWSThread extends JWS1Thr
       * 
       * @return null or { Alignment(+features and annotation), NewickFile)}
       */
-     public Object[] getAlignment(Alignment dataset,
+     public Object[] getAlignment(AlignmentI dataset,
 -            Map<String, Object> featureColours)
 +            Map<String, FeatureColourI> featureColours)
      {
  
        if (result != null && result.isFinished())