From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 14 Dec 2018 16:34:01 +0000 (+0000)
Subject: JAL-3171 raise warning when a dataset reference exists *and* a different dataset... 
X-Git-Tag: Release_2_11_1_0~78^2~12
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e837aa274d86db61848aeb6990eaa09c0c1e6a20;p=jalview.git

JAL-3171 raise warning when a dataset reference exists *and* a different dataset exists for the sequenceSetID
---

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 8c3175f..4cc43d3 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -5221,16 +5221,19 @@ public class Jalview2XML
     jalview.datamodel.AlignmentI ds = getDatasetFor(
             vamsasSet.getDatasetId());
     Vector dseqs = null;
-    if (ds == null)
+    if (!ignoreUnrefed)
     {
-      if (!ignoreUnrefed)
+      // recovering an alignment View
+      AlignmentI seqSetDS = getDatasetFor(UNIQSEQSETID + uniqueSeqSetId);
+      if (seqSetDS != null)
       {
-        // try to resolve the dataset via uniqueSeqSetId
-        ds = getDatasetFor(UNIQSEQSETID + uniqueSeqSetId);
-        if (ds != null)
+        if (ds != null && ds != seqSetDS)
         {
-          addDatasetRef(vamsasSet.getDatasetId(), ds);
+          warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
+                  + " - CDS/Protein crossreference data may be lost");
         }
+        ds = seqSetDS;
+        addDatasetRef(vamsasSet.getDatasetId(), ds);
       }
     }
     if (ds == null)