JAL-1824 corrected copy'n'paste error introduced from JAL-1821 refactor which causes...

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 2ba4427..5699d9e 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -20,27 +20,6 @@
  */
 package jalview.gui;
 
-import java.awt.Color;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Hashtable;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-import java.util.Vector;
-
-import javax.swing.ButtonGroup;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JColorChooser;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.JPopupMenu;
-import javax.swing.JRadioButtonMenuItem;
-
 import jalview.analysis.AAFrequency;
 import jalview.analysis.AlignmentAnnotationUtils;
 import jalview.analysis.AlignmentUtils;
@@ -80,6 +59,27 @@ import jalview.util.GroupUrlLink.UrlStringTooLongException;
 import jalview.util.MessageManager;
 import jalview.util.UrlLink;
 
+import java.awt.Color;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Hashtable;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+import java.util.Vector;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JColorChooser;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPopupMenu;
+import javax.swing.JRadioButtonMenuItem;
+
 /**
  * DOCUMENT ME!
  * 
@@ -204,7 +204,7 @@ public class PopupMenu extends JPopupMenu
 
   JMenu jMenu1 = new JMenu();
 
-  JMenuItem proteinStructureMenu = new JMenuItem();
+  JMenuItem pdbStructureDialog = new JMenuItem();
 
   JMenu rnaStructureMenu = new JMenu();
 
@@ -328,6 +328,7 @@ public class PopupMenu extends JPopupMenu
       }
       else
       {
+        int origCount = rnaStructureMenu.getItemCount();
         /*
          * add menu items to 2D-render any alignment or sequence secondary
          * structure annotation
@@ -343,17 +344,16 @@ 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 +361,6 @@ public class PopupMenu extends JPopupMenu
           }
         }
 
-
         if (seq.getAnnotation() != null)
         {
           AlignmentAnnotation seqAnns[] = seq.getAnnotation();
@@ -383,15 +382,17 @@ 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);
             }
           }
         }
+        if (rnaStructureMenu.getItemCount() == origCount)
+        {
+          remove(rnaStructureMenu);
+        }
       }
 
       menuItem = new JMenuItem(
@@ -604,7 +605,7 @@ public class PopupMenu extends JPopupMenu
     if (seq == null)
     {
       sequenceMenu.setVisible(false);
-      proteinStructureMenu.setVisible(false);
+      pdbStructureDialog.setVisible(false);
       rnaStructureMenu.setVisible(false);
     }
 
@@ -1346,9 +1347,9 @@ public class PopupMenu extends JPopupMenu
       }
     });
     jMenu1.setText(MessageManager.getString("label.group"));
-    proteinStructureMenu.setText(MessageManager
-            .getString("label.view_protein_structure"));
-    proteinStructureMenu.addActionListener(new ActionListener()
+    pdbStructureDialog.setText(MessageManager
+            .getString("label.show_pdbstruct_dialog"));
+    pdbStructureDialog.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent actionEvent)
@@ -1409,7 +1410,7 @@ public class PopupMenu extends JPopupMenu
     add(groupMenu);
     add(sequenceMenu);
     add(rnaStructureMenu);
-    add(proteinStructureMenu);
+    add(pdbStructureDialog);
     if (sequence!=null)
     {
       add(hideInsertions);
@@ -2401,8 +2402,8 @@ 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()