JAL-1114 - refactor methods handling Vectors and Hashtables to Lists and Maps, and...

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 6139764..c1bbc8d 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -270,14 +270,14 @@ public class PopupMenu extends JPopupMenu
           if (aa[i].getRNAStruc() != null)
           {
             final String rnastruc = aa[i].getRNAStruc();
-            
+            final String structureLine=aa[i].label;
             menuItem = new JMenuItem();
-            menuItem.setText("RNA structure - consensus");
+            menuItem.setText("2D RNA "+structureLine);
             menuItem.addActionListener(new java.awt.event.ActionListener()
             {
               public void actionPerformed(ActionEvent e)
               {
-                new AppVarna(seq, seq.getSequenceAsString(), rnastruc, seq
+                new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq
                         .getName(), ap);
               }
             });
@@ -298,13 +298,13 @@ public class PopupMenu extends JPopupMenu
               
            // TODO: make rnastrucF a bit more nice
               menuItem = new JMenuItem();
-              menuItem.setText("RNA structure - "+seq.getName());
+              menuItem.setText("2D RNA - "+seq.getName());
               menuItem.addActionListener(new java.awt.event.ActionListener()
               {
                 public void actionPerformed(ActionEvent e)
                 {
                   // TODO: VARNA does'nt print gaps in the sequence
-                  new AppVarna(seq,seq.getSequenceAsString(), rnastruc, seq
+                  new AppVarna(seq.getName()+" structure",seq,seq.getSequenceAsString(), rnastruc, seq
                           .getName(), ap);
                 }
               });
@@ -1289,8 +1289,7 @@ public class PopupMenu extends JPopupMenu
   {
     SequenceGroup sg = getGroup();
     sg.cs = new ClustalxColourScheme(
-            sg.getSequences(ap.av.getHiddenRepSequences()),
-            ap.av.getAlignment().getWidth());
+            sg,ap.av.getHiddenRepSequences());
     refresh();
   }