Merge branch 'pathc_JAL-1354' into develop

diff --combined src/jalview/jbgui/GAlignFrame.java
index 170f6b9,ee6ba9f..d95e1b1
--- 1/src/jalview/jbgui/GAlignFrame.java
--- 2/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@@ -140,8 -140,6 +140,8 @@@ public class GAlignFrame extends JInter
    protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
  
    protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
 +  
 +  protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
  
    // protected JRadioButtonMenuItem covariationColour = new
    // JRadioButtonMenuItem();
@@@ -460,7 -458,7 +460,7 @@@
      colours.add(purinePyrimidineColour);
      // colours.add(covariationColour);
      colours.add(tcoffeeColour);
 -
 +    colours.add(RNAInteractionColour);
      setColourSelected(jalview.bin.Cache
              .getDefault("DEFAULT_COLOUR", "None"));
  
@@@ -538,11 -536,6 +538,11 @@@
          purinePyrimidineColour.setSelected(true);
  
          break;
 +        
 +      case ColourSchemeProperty.RNAINTERACTION:
 +          RNAInteractionColour.setSelected(true);
 +
 +          break;
        /*
         * case ColourSchemeProperty.COVARIATION:
         * covariationColour.setSelected(true);
@@@ -930,15 -923,6 +930,15 @@@
                  purinePyrimidineColour_actionPerformed(e);
                }
              });
 +    
 +    RNAInteractionColour.setText("RNA Interaction type");
 +    RNAInteractionColour.addActionListener(new java.awt.event.ActionListener()
 +            {
 +              public void actionPerformed(ActionEvent e)
 +              {
 +                RNAInteractionColour_actionPerformed(e);
 +              }
 +            });
      /*
       * covariationColour.setText("Covariation");
       * covariationColour.addActionListener(new java.awt.event.ActionListener() {
@@@ -1042,7 -1026,7 +1042,7 @@@
          noColourmenuItem_actionPerformed(e);
        }
      });
-     wrapMenuItem.setText(MessageManager.getString("labe.wrap"));
+     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
      wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
      {
        public void actionPerformed(ActionEvent e)
@@@ -1915,7 -1899,6 +1915,7 @@@
      colourMenu.add(buriedColour);
      colourMenu.add(nucleotideColour);
      colourMenu.add(purinePyrimidineColour);
 +    colourMenu.add(RNAInteractionColour);
      // colourMenu.add(covariationColour);
      colourMenu.add(tcoffeeColour);
      colourMenu.add(userDefinedColour);
@@@ -1925,7 -1908,7 +1925,7 @@@
      colourMenu.add(abovePIDThreshold);
      colourMenu.add(modifyPID);
      colourMenu.add(annotationColour);
 -    colourMenu.add(rnahelicesColour);
 +    colourMenu.add(rnahelicesColour);  
      calculateMenu.add(sort);
      calculateMenu.add(calculateTree);
      calculateMenu.addSeparator();
@@@ -2312,11 -2295,6 +2312,11 @@@
    protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
    {
    }
 +  
 +  protected void RNAInteractionColour_actionPerformed(ActionEvent e)
 +  {
 +  }
 +  
  
    /*
     * protected void covariationColour_actionPerformed(ActionEvent e) { }