Merge branch 'develop' into features/JAL-2360colourSchemeApplicability

Conflicts:
	src/jalview/gui/UserDefinedColours.java

diff --cc src/jalview/gui/UserDefinedColours.java
index 012edb6,6b4bd10..5314c5c
--- 1/src/jalview/gui/UserDefinedColours.java
--- 2/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@@ -64,12 -60,6 +64,13 @@@ 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";
 +
 +  private static final String LAST_DIRECTORY = "LAST_DIRECTORY";
 +
    private static final int MY_FRAME_HEIGHT = 420;
  
    private static final int MY_FRAME_WIDTH = 810;
@@@ -150,7 -142,7 +151,8 @@@
  
      if (oldColourScheme instanceof UserColourScheme)
      {
-       schemeName.setText(((UserColourScheme) oldColourScheme).getSchemeName());
 -      schemeName.setText(((UserColourScheme) oldColourScheme).getName());
++      schemeName.setText(((UserColourScheme) oldColourScheme)
++              .getSchemeName());
      }
  
      resetButtonPanel(false);
@@@ -389,22 -383,15 +391,22 @@@
    }
  
    /**
 -   * DOCUMENT ME!
 +   * A helper method to update or make a colour button, whose background colour
 +   * is the associated colour, and text colour a darker shade of the same. If
 +   * the button is already in the list, then its text and margins are updated,
 +   * if not then it is created and added. This method supports toggling between
 +   * case-sensitive and case-insensitive button panels. The case-sensitive
 +   * version has abbreviated button text in order to fit in more buttons.
     * 
     * @param label
 -   *          DOCUMENT ME!
 -   * @param aa
 -   *          DOCUMENT ME!
 +   * @param residue
 +   * @param the
 +   *          list of buttons
 +   * @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 aa,
 -          ArrayList<JButton> caseSensitiveButtons, int buttonIndex)
++  JButton makeButton(String label, String residue, List<JButton> buttons,
++          int buttonIndex)
    {
      final JButton button;
      Color col;
@@@ -614,42 -605,50 +616,43 @@@
  
      int value = chooser.showOpenDialog(this);
  
 -    if (value == JalviewFileChooser.APPROVE_OPTION)
 +    if (value != JalviewFileChooser.APPROVE_OPTION)
      {
 -      File choice = chooser.getSelectedFile();
 -      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
 -      String defaultColours = jalview.bin.Cache.getDefault(
 -              "USER_DEFINED_COLOURS", choice.getPath());
 -      if (defaultColours.indexOf(choice.getPath()) == -1)
 -      {
 -        defaultColours = defaultColours.concat("|")
 -                .concat(choice.getPath());
 -      }
 -
 -      jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
 -
 -      UserColourScheme ucs = loadColours(choice.getAbsolutePath());
 -      Color[] colors = ucs.getColours();
 -      schemeName.setText(ucs.getName());
 +      return;
 +    }
 +    File choice = chooser.getSelectedFile();
 +    Cache.setProperty(LAST_DIRECTORY, choice.getParent());
  
-     UserColourScheme ucs = ColourSchemes.loadColourScheme(choice.getAbsolutePath());
 -      if (ucs.getLowerCaseColours() != null)
 -      {
 -        caseSensitive.setSelected(true);
 -        lcaseColour.setEnabled(true);
 -        resetButtonPanel(true);
 -        for (int i = 0; i < lowerCaseButtons.size(); i++)
 -        {
 -          JButton button = lowerCaseButtons.get(i);
 -          button.setBackground(ucs.getLowerCaseColours()[i]);
 -        }
++    UserColourScheme ucs = ColourSchemes.loadColourScheme(choice
++            .getAbsolutePath());
 +    Color[] colors = ucs.getColours();
 +    schemeName.setText(ucs.getSchemeName());
  
 -      }
 -      else
 +    if (ucs.getLowerCaseColours() != null)
 +    {
 +      caseSensitive.setSelected(true);
 +      lcaseColour.setEnabled(true);
 +      resetButtonPanel(true);
 +      for (int i = 0; i < lowerCaseButtons.size(); i++)
        {
 -        caseSensitive.setSelected(false);
 -        lcaseColour.setEnabled(false);
 -        resetButtonPanel(false);
 -      }
 -
 -      for (int i = 0; i < upperCaseButtons.size(); i++)
 -      {
 -        JButton button = upperCaseButtons.get(i);
 -        button.setBackground(colors[i]);
 +        JButton button = lowerCaseButtons.get(i);
 +        button.setBackground(ucs.getLowerCaseColours()[i]);
        }
 +    }
 +    else
 +    {
 +      caseSensitive.setSelected(false);
 +      lcaseColour.setEnabled(false);
 +      resetButtonPanel(false);
 +    }
  
 +    for (int i = 0; i < upperCaseButtons.size(); i++)
 +    {
 +      JButton button = upperCaseButtons.get(i);
 +      button.setBackground(colors[i]);
      }
 +
 +    addNewColourScheme(choice.getPath());
    }
  
    /**
@@@ -711,14 -827,13 +714,13 @@@
        {
          return;
        }
 -
 -      userColourSchemes.remove(schemeName.getText());
 +      ColourSchemes.getInstance().removeColourScheme(name);
      }
-     JalviewFileChooser chooser = new JalviewFileChooser(
-             Cache.getProperty(LAST_DIRECTORY), "jc",
+     JalviewFileChooser chooser = new JalviewFileChooser("jc",
              "Jalview User Colours");
  
 -    chooser.setFileView(new JalviewFileView());
 +    JalviewFileView fileView = new JalviewFileView();
 +    chooser.setFileView(fileView);
      chooser.setDialogTitle(MessageManager
              .getString("label.save_colour_scheme"));
      chooser.setToolTipText(MessageManager.getString("action.save"));