X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=0095bc967eea1cb9cb6647cca9be48ecffae78bd;hb=21fccb30635d61dbf7ad0f266a88f07fb87358f7;hp=1263b712e6395c2568e7331c63e8b5f0c81e51d6;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 1263b71..0095bc9 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -204,9 +204,9 @@ public class PopupMenu extends JPopupMenu
 
   JMenu jMenu1 = new JMenu();
 
-  JMenuItem structureMenu = new JMenuItem();
+  JMenuItem proteinStructureMenu = new JMenuItem();
 
-  JMenu viewStructureMenu = new JMenu();
+  JMenu rnaStructureMenu = new JMenu();
 
   JMenuItem editSequence = new JMenuItem();
 
@@ -322,89 +322,54 @@ public class PopupMenu extends JPopupMenu
         makeReferenceSeq.setText("Mark as representative");
       }
 
-      if (seq.getDatasetSequence().getPDBId() != null
-              && seq.getDatasetSequence().getPDBId().size() > 0)
+      if (!ap.av.getAlignment().isNucleotide())
       {
-        java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
-                .elements();
-
-        while (e.hasMoreElements())
-        {
-          final PDBEntry pdb = (PDBEntry) e.nextElement();
-
-          menuItem = new JMenuItem();
-          menuItem.setText(pdb.getId());
-          menuItem.addActionListener(new ActionListener()
-          {
-            @Override
-            public void actionPerformed(ActionEvent e)
-            {
-              // TODO re JAL-860: optionally open dialog or provide a menu entry
-              // allowing user to open just one structure per sequence
-              // new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
-              // { pdb })[0], null, ap);
-              new StructureViewer(ap.getStructureSelectionManager())
-                      .viewStructures(pdb,
-                              ap.av.collateForPDB(new PDBEntry[]
-                              { pdb })[0], null, ap);
-            }
-          });
-          viewStructureMenu.add(menuItem);
-
-          /*
-           * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
-           * menuItem.addActionListener(new java.awt.event.ActionListener() {
-           * public void actionPerformed(ActionEvent e) {
-           * colourByStructure(pdb.getId()); } });
-           * colStructureMenu.add(menuItem);
-           */
-        }
+        remove(rnaStructureMenu);
       }
       else
       {
-        if (ap.av.getAlignment().isNucleotide() == false)
-        {
-          structureMenu.remove(viewStructureMenu);
-        }
-      }
-      if (ap.av.getAlignment().isNucleotide() == true)
-      {
-        AlignmentAnnotation[] aa = ap.av.getAlignment()
+        /*
+         * 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");
-              }
-            });
-            viewStructureMenu.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(
@@ -416,13 +381,10 @@ 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);
                 }
               });
-              viewStructureMenu.add(menuItem);
+              rnaStructureMenu.add(menuItem);
             }
           }
         }
@@ -638,7 +600,8 @@ public class PopupMenu extends JPopupMenu
     if (seq == null)
     {
       sequenceMenu.setVisible(false);
-      structureMenu.setVisible(false);
+      proteinStructureMenu.setVisible(false);
+      rnaStructureMenu.setVisible(false);
     }
 
     if (links != null && links.size() > 0)
@@ -1379,8 +1342,9 @@ public class PopupMenu extends JPopupMenu
       }
     });
     jMenu1.setText(MessageManager.getString("label.group"));
-    structureMenu.setText(MessageManager.getString("label.view_structure"));
-    structureMenu.addActionListener(new ActionListener()
+    proteinStructureMenu.setText(MessageManager
+            .getString("label.view_protein_structure"));
+    proteinStructureMenu.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent actionEvent)
@@ -1395,8 +1359,9 @@ public class PopupMenu extends JPopupMenu
       }
     });
 
-    viewStructureMenu.setText(MessageManager
-            .getString("label.view_structure"));
+    rnaStructureMenu.setText(MessageManager
+            .getString("label.view_rna_structure"));
+
     // colStructureMenu.setText("Colour By Structure");
     editSequence.setText(MessageManager.getString("label.edit_sequence")
             + "...");
@@ -1439,7 +1404,8 @@ public class PopupMenu extends JPopupMenu
     groupMenu.add(sequenceSelDetails);
     add(groupMenu);
     add(sequenceMenu);
-    add(structureMenu);
+    add(rnaStructureMenu);
+    add(proteinStructureMenu);
     if (sequence!=null)
     {
       add(hideInsertions);