From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 28 Sep 2016 13:24:48 +0000 (+0100)
Subject: JAL-2210 instrument setDBRefs to call ensurePrimaries
X-Git-Tag: Release_2_10_0~20^2~31
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1c5971e6df15c0d5c774a2cb7dbdac286a72a9b2;p=jalview.git

JAL-2210 instrument setDBRefs to call ensurePrimaries
JAL-2210 defer setDBRefs to datasetSequence if available
---

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 6b57ef7..d295480 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -944,7 +944,17 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public void setDBRefs(DBRefEntry[] dbref)
   {
+    if (dbrefs == null && datasetSequence != null
+            && this != datasetSequence)
+    {
+      datasetSequence.setDBRefs(dbref);
+      return;
+    }
     dbrefs = dbref;
+    if (dbrefs != null)
+    {
+      DBRefUtils.ensurePrimaries(this);
+    }
   }
 
   @Override
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index b7a291e..a29e2ba 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -314,6 +314,14 @@ public interface SequenceI extends ASequenceI
 
   public void setVamsasId(String id);
 
+  /**
+   * set the array of Database references for the sequence.
+   * 
+   * @param dbs
+   * @deprecated - use is discouraged since side-effects may occur if DBRefEntry
+   *             set are not normalised.
+   */
+  @Deprecated
   public void setDBRefs(DBRefEntry[] dbs);
 
   public DBRefEntry[] getDBRefs();