X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=c4612106e93c703352adebe52522796316df9dd9;hb=817f6a0616bc319e28801ba545fae3c8907bacbc;hp=3a9060eb30471500b6a75d312640adf1f0047c56;hpb=23857aedb7848e47e5cb6336a5f4acf269b6e13a;p=jalview.git

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 3a9060e..c461210 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -3098,8 +3098,6 @@ public class Jalview2XML
       }
 
       if (safeBoolean(jseq.isViewreference()))
-      // if (jseq.isViewreference() != null
-      // && jseq.isViewreference().booleanValue())
       {
         referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
       }
@@ -3385,8 +3383,7 @@ public class Jalview2XML
           // annotation.setAutoCalculated(true);
           // }
         }
-        if (autoForView || // (annotation.hasAutoCalculated() &&
-                annotation.isAutoCalculated())
+        if (autoForView || annotation.isAutoCalculated())
         {
           // remove ID - we don't recover annotation from other views for
           // view-specific annotation
@@ -5566,6 +5563,10 @@ public class Jalview2XML
     initSeqRefs();
     JalviewModel jm = saveState(ap, null, null, null);
 
+    addDatasetRef(
+            jm.getVamsasModel().getSequenceSet().get(0).getDatasetId(),
+            ap.getAlignment().getDataset());
+
     uniqueSetSuffix = "";
     // jm.getJalviewModelSequence().getViewport(0).setId(null);
     jm.getViewport().get(0).setId(null);