Merge branch 'develop' into features/JAL-892varnaToProject

[jalview.git] / src / jalview / gui / PopupMenu.java

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 2ba4427..ad3d6af 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -343,17 +343,16 @@ public class PopupMenu extends JPopupMenu
               /*
                * valid alignment RNA secondary structure annotation
                */
-              final String structureLine = aa.label + " (alignment)";
               menuItem = new JMenuItem();
               menuItem.setText(MessageManager.formatMessage(
                       "label.2d_rna_structure_line", new Object[]
-                      { structureLine }));
+                      { aa.label }));
               menuItem.addActionListener(new java.awt.event.ActionListener()
               {
                 @Override
                 public void actionPerformed(ActionEvent e)
                 {
-                  new AppVarna(structureLine, seq, aa, ap);
+                  new AppVarna(seq, aa, ap);
                 }
               });
               rnaStructureMenu.add(menuItem);
@@ -361,7 +360,6 @@ public class PopupMenu extends JPopupMenu
           }
         }
 
-
         if (seq.getAnnotation() != null)
         {
           AlignmentAnnotation seqAnns[] = seq.getAnnotation();
@@ -383,9 +381,7 @@ public class PopupMenu extends JPopupMenu
                 public void actionPerformed(ActionEvent e)
                 {
                   // TODO: VARNA does'nt print gaps in the sequence
-
-                  new AppVarna(seq.getName() + " structure", seq, aa,
-                          ap);
+                  new AppVarna(seq, aa, ap);
                 }
               });
               rnaStructureMenu.add(menuItem);
@@ -2401,8 +2397,8 @@ public class PopupMenu extends JPopupMenu
     // or we simply trust the user wants
     // wysiwig behaviour
 
-    cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
-            ap.av, true));
+    cap.setText(new FormatAdapter(ap).formatSequences(e.getActionCommand(),
+            ap, true));
   }
 
   public void pdbFromFile_actionPerformed()