X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;h=dcc5f269dd0ca57654ae8c3053ec12cb625ecebf;hb=4660fcf0745dbc1f6f6e7241b398301f93edb548;hp=929e56efdeebe3645c1c48b1118c9e047f659324;hpb=fd9ed8df6a98c86228100aa4e9d6698c87a61c08;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 929e56e..dcc5f26 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -272,8 +272,13 @@ public class HiddenSequences
         index++;
       }
     }
+    Alignment fAlignmt = new Alignment(seq);
+    fAlignmt.annotations = alignment.getAlignmentAnnotation();
+    fAlignmt.alignmentProperties = alignment.getProperties();
+    fAlignmt.groups = alignment.getGroups();
+    fAlignmt.hasRNAStructure = alignment.hasRNAStructure();
 
-    return new Alignment(seq);
+    return fAlignmt;
   }
 
   public boolean isHidden(SequenceI seq)