Merge branch 'develop' into features/JAL-3010ontologyFeatureSettings

diff --cc src/jalview/gui/FeatureTypeSettings.java
index 7aef644,55bc519..9609996
--- 1/src/jalview/gui/FeatureTypeSettings.java
--- 2/src/jalview/gui/FeatureTypeSettings.java
+++ b/src/jalview/gui/FeatureTypeSettings.java
@@@ -237,45 -217,11 +237,31 @@@ public class FeatureTypeSettings extend
      this.fr = frender;
      this.featureType = theType;
      ap = fr.ap;
 -    originalFilter = fr.getFeatureFilter(theType);
 -    originalColour = fr.getFeatureColours().get(theType);
 -    
 +
 +    /*
 +     * determine sub-types (if any) of this feature type
 +     */
 +    List<String> types = fr.getRenderOrder();
 +    subTypes = SequenceOntologyFactory.getInstance()
 +            .getChildTerms(this.featureType, types);
 +    Collections.sort(subTypes); // sort for ease of reading in tooltip
 +
 +    /*
 +     * save original colours and filters for this feature type
 +     * and any sub-types, to restore on Cancel
 +     */
 +    originalFilters = new HashMap<>();
 +    originalFilters.put(theType, fr.getFeatureFilter(theType));
 +    originalColours = new HashMap<>();
 +    originalColours.put(theType, fr.getFeatureColours().get(theType));
 +    for (String child : subTypes)
 +    {
 +      originalFilters.put(child, fr.getFeatureFilter(child));
 +      originalColours.put(child, fr.getFeatureColours().get(child));
 +    }
 +
      adjusting = true;
- 
+     
      try
      {
        initialise();
@@@ -1319,15 -1177,8 +1311,13 @@@
     */
    private JPanel initialiseAndOrPanel()
    {
 -    JPanel andOrPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
 +    JPanel andOrPanel = new JPanel(new BorderLayout());
      andOrPanel.setBackground(Color.white);
- //<<<<<<< HEAD
++
 +//    JPanel panel1 = new JPanel(new FlowLayout(FlowLayout.LEFT));
 +//    andOrPanel.add(panel1, BorderLayout.WEST);
 +//    panel1.setBackground(Color.white);
 +//    panel1.setBorder(BorderFactory.createLineBorder(debugBorderColour));
- //=======
- //>>>>>>> refs/heads/develop
      andFilters = new JRadioButton(MessageManager.getString("label.and"));
      orFilters = new JRadioButton(MessageManager.getString("label.or"));
      ActionListener actionListener = new ActionListener()