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 0d28a70..5699d9e 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -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();
 
@@ -322,49 +322,55 @@ public class PopupMenu extends JPopupMenu
         makeReferenceSeq.setText("Mark as representative");
       }
 
-      if (ap.av.getAlignment().isNucleotide() == false)
+      if (!ap.av.getAlignment().isNucleotide())
       {
         remove(rnaStructureMenu);
       }
-
-      if (ap.av.getAlignment().isNucleotide() == true)
+      else
       {
-        AlignmentAnnotation[] aa = ap.av.getAlignment()
+        int origCount = rnaStructureMenu.getItemCount();
+        /*
+         * add menu items to 2D-render any alignment or sequence secondary
+         * structure annotation
+         */
+        AlignmentAnnotation[] aas = ap.av.getAlignment()
                 .getAlignmentAnnotation();
-        for (int i = 0; aa != null && i < aa.length; i++)
+        if (aas != null)
         {
-          if (aa[i].isValidStruc() && aa[i].sequenceRef == null)
+          for (final AlignmentAnnotation aa : aas)
           {
-            final String rnastruc = aa[i].getRNAStruc();
-            final String structureLine = aa[i].label + " (alignment)";
-            menuItem = new JMenuItem();
-            menuItem.setText(MessageManager.formatMessage(
-                    "label.2d_rna_structure_line", new Object[]
-                    { structureLine }));
-            menuItem.addActionListener(new java.awt.event.ActionListener()
+            if (aa.isValidStruc() && aa.sequenceRef == null)
             {
-              @Override
-              public void actionPerformed(ActionEvent e)
+              /*
+               * valid alignment RNA secondary structure annotation
+               */
+              menuItem = new JMenuItem();
+              menuItem.setText(MessageManager.formatMessage(
+                      "label.2d_rna_structure_line", new Object[]
+                      { aa.label }));
+              menuItem.addActionListener(new java.awt.event.ActionListener()
               {
-                new AppVarna(structureLine, seq, seq.getSequenceAsString(),
-                        rnastruc, seq.getName(), ap);
-                System.out.println("end");
-              }
-            });
-            rnaStructureMenu.add(menuItem);
+                @Override
+                public void actionPerformed(ActionEvent e)
+                {
+                  new AppVarna(seq, aa, ap);
+                }
+              });
+              rnaStructureMenu.add(menuItem);
+            }
           }
         }
 
-
         if (seq.getAnnotation() != null)
         {
-          AlignmentAnnotation seqAnno[] = seq.getAnnotation();
-          for (int i = 0; i < seqAnno.length; i++)
+          AlignmentAnnotation seqAnns[] = seq.getAnnotation();
+          for (final AlignmentAnnotation aa : seqAnns)
           {
-            if (seqAnno[i].isValidStruc())
+            if (aa.isValidStruc())
             {
-              final String rnastruc = seqAnno[i].getRNAStruc();
-
+              /*
+               * valid sequence RNA secondary structure annotation
+               */
               // TODO: make rnastrucF a bit more nice
               menuItem = new JMenuItem();
               menuItem.setText(MessageManager.formatMessage(
@@ -376,16 +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, seq
-                          .getSequenceAsString(), rnastruc, seq.getName(),
-                          ap);
+                  new AppVarna(seq, aa, ap);
                 }
               });
               rnaStructureMenu.add(menuItem);
             }
           }
         }
+        if (rnaStructureMenu.getItemCount() == origCount)
+        {
+          remove(rnaStructureMenu);
+        }
       }
 
       menuItem = new JMenuItem(
@@ -598,7 +605,7 @@ public class PopupMenu extends JPopupMenu
     if (seq == null)
     {
       sequenceMenu.setVisible(false);
-      proteinStructureMenu.setVisible(false);
+      pdbStructureDialog.setVisible(false);
       rnaStructureMenu.setVisible(false);
     }
 
@@ -1340,9 +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)
@@ -1403,7 +1410,7 @@ public class PopupMenu extends JPopupMenu
     add(groupMenu);
     add(sequenceMenu);
     add(rnaStructureMenu);
-    add(proteinStructureMenu);
+    add(pdbStructureDialog);
     if (sequence!=null)
     {
       add(hideInsertions);
@@ -2395,8 +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()