Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371colle...

diff --combined src/jalview/gui/UserDefinedColours.java
index a368e74,5314c5c..7a5c1f1
--- 1/src/jalview/gui/UserDefinedColours.java
--- 2/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@@ -64,7 -64,8 +64,8 @@@ import javax.swing.event.ChangeListener
  public class UserDefinedColours extends GUserDefinedColours implements
          ChangeListener
  {
-   private static final Font VERDANA_BOLD_10 = new Font("Verdana", Font.BOLD, 10);
+   private static final Font VERDANA_BOLD_10 = new Font("Verdana",
+           Font.BOLD, 10);
  
    public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
  
@@@ -109,7 -110,7 +110,7 @@@
  
      if (seqGroup != null)
      {
 -      oldColourScheme = seqGroup.cs;
 +      oldColourScheme = seqGroup.getColourScheme();
      }
      else
      {
@@@ -150,7 -151,8 +151,8 @@@
  
      if (oldColourScheme instanceof UserColourScheme)
      {
-       schemeName.setText(((UserColourScheme) oldColourScheme).getSchemeName());
+       schemeName.setText(((UserColourScheme) oldColourScheme)
+               .getSchemeName());
      }
  
      resetButtonPanel(false);
@@@ -403,8 -405,8 +405,8 @@@
     * @param buttonIndex
     *          the button's position in the list
     */
-   JButton makeButton(String label, String residue,
-           List<JButton> buttons, int buttonIndex)
+   JButton makeButton(String label, String residue, List<JButton> buttons,
+           int buttonIndex)
    {
      final JButton button;
      Color col;
@@@ -435,8 -437,7 +437,8 @@@
        col = Color.white;
        if (oldColourScheme != null && oldColourScheme.isSimple())
        {
 -        col = oldColourScheme.findColour(residue.charAt(0));
 +        col = oldColourScheme.findColour(residue.charAt(0), 0, null, null,
 +                0f);
        }
      }
  
@@@ -522,7 -523,7 +524,7 @@@
  
      if (seqGroup != null)
      {
 -      seqGroup.cs = ucs;
 +      seqGroup.setColourScheme(ucs);
        ap.paintAlignment(true);
      }
      else if (ap != null)
@@@ -586,10 -587,10 +588,10 @@@
        ucs.setLowerCaseColours(newColours);
      }
  
 -    if (ap != null)
 -    {
 -      ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
 -    }
 +    // if (ap != null)
 +    // {
 +    // ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
 +    // }
  
      return ucs;
    }
@@@ -606,8 -607,8 +608,8 @@@
      upperCaseButtons = new ArrayList<JButton>();
      lowerCaseButtons = new ArrayList<JButton>();
  
-     JalviewFileChooser chooser = new JalviewFileChooser(
-             Cache.getProperty(LAST_DIRECTORY), "jc", "Jalview User Colours");
+     JalviewFileChooser chooser = new JalviewFileChooser("jc",
+             "Jalview User Colours");
      chooser.setFileView(new JalviewFileView());
      chooser.setDialogTitle(MessageManager
              .getString("label.load_colour_scheme"));
@@@ -622,7 -623,8 +624,8 @@@
      File choice = chooser.getSelectedFile();
      Cache.setProperty(LAST_DIRECTORY, choice.getParent());
  
-     UserColourScheme ucs = ColourSchemes.loadColourScheme(choice.getAbsolutePath());
+     UserColourScheme ucs = ColourSchemes.loadColourScheme(choice
+             .getAbsolutePath());
      Color[] colors = ucs.getColours();
      schemeName.setText(ucs.getSchemeName());
  
@@@ -714,8 -716,7 +717,7 @@@
        }
        ColourSchemes.getInstance().removeColourScheme(name);
      }
-     JalviewFileChooser chooser = new JalviewFileChooser(
-             Cache.getProperty(LAST_DIRECTORY), "jc",
+     JalviewFileChooser chooser = new JalviewFileChooser("jc",
              "Jalview User Colours");
  
      JalviewFileView fileView = new JalviewFileView();
@@@ -821,7 -822,7 +823,7 @@@
      {
        if (seqGroup != null)
        {
 -        seqGroup.cs = oldColourScheme;
 +        seqGroup.setColourScheme(oldColourScheme);
        }
        else
        {