Merge branch 'JAL-1397' into develop

diff --combined src/jalview/gui/PopupMenu.java
index d892bc7,3bc7c5c..037f007
--- 1/src/jalview/gui/PopupMenu.java
--- 2/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@@ -70,7 -70,6 +70,7 @@@ public class PopupMenu extends JPopupMe
    protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  
    protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
 +  protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
  
    // protected JRadioButtonMenuItem covariationColour = new
    // JRadioButtonMenuItem();
@@@ -122,11 -121,7 +122,11 @@@
    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();
@@@ -197,7 -192,6 +197,7 @@@
      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++)
@@@ -286,23 -280,11 +286,23 @@@
              menuItem = new JMenuItem();
              menuItem.setText("2D RNA " + structureLine);
              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);
@@@ -328,7 -310,6 +328,7 @@@
                  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);
@@@ -466,8 -447,6 +466,8 @@@
        {
          purinePyrimidineColour.setSelected(true);
        }
 +      
 +   
        /*
         * else if (sg.cs instanceof CovariationColourScheme) {
         * covariationColour.setSelected(true); }
@@@ -1074,32 -1053,6 +1074,32 @@@
          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("Enter PDB Id");
      enterPDB.addActionListener(new ActionListener()
      {
@@@ -1177,10 -1130,9 +1177,10 @@@
      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);
@@@ -1215,9 -1167,6 +1215,9 @@@
      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);
@@@ -1345,8 -1294,6 +1345,8 @@@
                  purinePyrimidineColour_actionPerformed();
                }
              });
 +    
 +   
      /*
       * covariationColour.addActionListener(new java.awt.event.ActionListener() {
       * public void actionPerformed(ActionEvent e) {
@@@ -1534,7 -1481,6 +1534,7 @@@
      refresh();
    }
  
 +
    /*
     * protected void covariationColour_actionPerformed() { getGroup().cs = new
     * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
@@@ -1696,7 -1642,7 +1696,7 @@@
              sequence.getAnnotation()[0], null,
              AnnotationColourGradient.NO_THRESHOLD);
  
-     acg.predefinedColours = true;
+     acg.setPredefinedColours(true);
      sg.cs = acg;
  
      refresh();
@@@ -2014,18 -1960,7 +2014,18 @@@
      }
  
    }
 -
 +    // 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,