X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=8467c660a36da0107be14dc4a88b9566613bf32c;hb=a17560ede81e39f8dba0c6d6c3fa7ccb689a124e;hp=1c7be464b88154657ea2c65f1fb8c33ec8061cc7;hpb=8c0f33de9bd3c211883eddcc313ebc7978f7b0b5;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 1c7be46..8467c66 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -372,12 +372,12 @@ public class PopupMenu extends JPopupMenu
       {
         AlignmentAnnotation[] aa = ap.av.getAlignment()
                 .getAlignmentAnnotation();
-        for (int i = 0; i < aa.length; i++)
+        for (int i = 0; aa != null && i < aa.length; i++)
         {
-          if (aa[i].getRNAStruc() != null)
+          if (aa[i].isValidStruc() && aa[i].sequenceRef == null)
           {
             final String rnastruc = aa[i].getRNAStruc();
-            final String structureLine = aa[i].label;
+            final String structureLine = aa[i].label + " (alignment)";
             menuItem = new JMenuItem();
             menuItem.setText(MessageManager.formatMessage(
                     "label.2d_rna_structure_line", new String[]
@@ -414,7 +414,7 @@ public class PopupMenu extends JPopupMenu
           AlignmentAnnotation seqAnno[] = seq.getAnnotation();
           for (int i = 0; i < seqAnno.length; i++)
           {
-            if (seqAnno[i].getRNAStruc() != null)
+            if (seqAnno[i].isValidStruc())
             {
               final String rnastruc = seqAnno[i].getRNAStruc();