Merge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 67bc00f..742cd6b 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -72,6 +72,7 @@ public class PopupMenu extends JPopupMenu
   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 
   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
 
   // protected JRadioButtonMenuItem covariationColour = new
   // JRadioButtonMenuItem();
@@ -123,7 +124,11 @@ public class PopupMenu extends JPopupMenu
   JMenu pdbMenu = new JMenu();
 
   JMenuItem pdbFromFile = new JMenuItem();
-
+    // JBPNote: Commented these out - Should add these services via the web services menu system.
+    // JMenuItem ContraFold = new JMenuItem();
+  
+    // JMenuItem RNAFold = new JMenuItem();
+  
   JMenuItem enterPDB = new JMenuItem();
 
   JMenuItem discoverPDB = new JMenuItem();
@@ -194,6 +199,7 @@ public class PopupMenu extends JPopupMenu
     colours.add(PIDColour);
     colours.add(BLOSUM62Colour);
     colours.add(purinePyrimidineColour);
+    colours.add(RNAInteractionColour);
     // colours.add(covariationColour);
 
     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
@@ -282,11 +288,23 @@ public class PopupMenu extends JPopupMenu
             menuItem = new JMenuItem();
             menuItem.setText(MessageManager.formatMessage("label.2d_rna_structure_line", new String[]{structureLine}));\r
             menuItem.addActionListener(new java.awt.event.ActionListener()
+            
             {
               public void actionPerformed(ActionEvent e)
               {
-                new AppVarna(structureLine, seq, seq.getSequenceAsString(),
-                        rnastruc, seq.getName(), ap);
+                       //System.out.println("1:"+structureLine);
+                       System.out.println("1:sname"+seq.getName());
+                       System.out.println("2:seq"+seq);
+                
+                       //System.out.println("3:"+seq.getSequenceAsString());
+                       System.out.println("3:strucseq"+rnastruc);
+                       //System.out.println("4:struc"+seq.getRNA());
+                       System.out.println("5:name"+seq.getName());
+                       System.out.println("6:ap"+ap);
+                       new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq
+                            .getName(), ap);
+                       //new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), seq.getName(), ap);
+                       System.out.println("end");
               }
             });
             viewStructureMenu.add(menuItem);
@@ -312,6 +330,7 @@ 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, seq
                           .getSequenceAsString(), rnastruc, seq.getName(),
                           ap);
@@ -449,6 +468,8 @@ public class PopupMenu extends JPopupMenu
       {
         purinePyrimidineColour.setSelected(true);
       }
+      
+   
       /*
        * else if (sg.cs instanceof CovariationColourScheme) {
        * covariationColour.setSelected(true); }
@@ -1061,6 +1082,32 @@ public class PopupMenu extends JPopupMenu
         pdbFromFile_actionPerformed();
       }
     });
+//    RNAFold.setText("From RNA Fold with predict2D");
+//    RNAFold.addActionListener(new ActionListener()
+//    {
+//      public void actionPerformed(ActionEvent e)
+//      {
+//       try {
+//                     RNAFold_actionPerformed();
+//             } catch (Exception e1) {
+//                     // TODO Auto-generated catch block
+//                     e1.printStackTrace();
+//             }
+//      }   
+//    });
+//    ContraFold.setText("From Contra Fold with predict2D");
+//    ContraFold.addActionListener(new ActionListener()
+//    {
+//      public void actionPerformed(ActionEvent e)
+//      {
+//       try {
+//                     ContraFold_actionPerformed();
+//             } catch (Exception e1) {
+//                     // TODO Auto-generated catch block
+//                     e1.printStackTrace();
+//             }
+//      }   
+//    });
     enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));\r
     enterPDB.addActionListener(new ActionListener()
     {
@@ -1138,9 +1185,10 @@ public class PopupMenu extends JPopupMenu
     colourMenu.add(turnColour);
     colourMenu.add(buriedColour);
     colourMenu.add(nucleotideMenuItem);
-    if (ap.getAlignment().isNucleotide())
-    {
-      colourMenu.add(purinePyrimidineColour);
+    if (ap.getAlignment().isNucleotide()) {
+       // JBPNote - commented since the colourscheme isn't functional
+       //  colourMenu.add(RNAInteractionColour);
+       colourMenu.add(purinePyrimidineColour);
     }
     // colourMenu.add(covariationColour);
     colourMenu.add(userDefinedColour);
@@ -1175,6 +1223,9 @@ public class PopupMenu extends JPopupMenu
     editMenu.add(lowerCase);
     editMenu.add(toggle);
     pdbMenu.add(pdbFromFile);
+    // JBPNote: These shouldn't be added here - should appear in a generic 'apply web service to this sequence menu'
+    //    pdbMenu.add(RNAFold);
+    //    pdbMenu.add(ContraFold);
     pdbMenu.add(enterPDB);
     pdbMenu.add(discoverPDB);
     jMenu1.add(groupName);
@@ -1302,6 +1353,8 @@ public class PopupMenu extends JPopupMenu
                 purinePyrimidineColour_actionPerformed();
               }
             });
+    
+   
     /*
      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
      * public void actionPerformed(ActionEvent e) {
@@ -1488,6 +1541,7 @@ public class PopupMenu extends JPopupMenu
     refresh();
   }
 
+
   /*
    * protected void covariationColour_actionPerformed() { getGroup().cs = new
    * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
@@ -1965,7 +2019,18 @@ public class PopupMenu extends JPopupMenu
     }
 
   }
-
+    // JBNote: commented out - these won't be instantiated here...!  
+//  public void RNAFold_actionPerformed() throws Exception
+//  {
+//       Predict2D P2D = new Predict2D();
+//       P2D.getStructure2DFromRNAFold("toto");
+//  }
+//  
+//  public void ContraFold_actionPerformed() throws Exception
+//  {
+//       Predict2D P2D = new Predict2D();
+//       P2D.getStructure2DFromContraFold("toto");
+//  }
   public void enterPDB_actionPerformed()
   {
     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,