From: Jim Procter <jprocter@dundee.ac.uk>
Date: Fri, 21 Nov 2014 08:54:11 +0000 (+0000)
Subject: JAL-1592 JAL-1489 avoid invalid RNA structure and distinguish alignment associated... 
X-Git-Tag: Jalview_2_9~148^2~16
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=a16e1965f87dc25c9d6bc6672fbf3a8ad703357e

JAL-1592 JAL-1489 avoid invalid RNA structure and distinguish alignment associated from sequence associated structure lines
---

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 1c7be46..36811c7 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -374,10 +374,10 @@ public class PopupMenu extends JPopupMenu
                 .getAlignmentAnnotation();
         for (int i = 0; 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();