Merge branch 'develop' into features/JAL-2446NCList

Conflicts:
	src/jalview/gui/FeatureRenderer.java

diff --cc src/jalview/gui/FeatureRenderer.java
index 0779760,55c4323..c0e3e73
--- 1/src/jalview/gui/FeatureRenderer.java
--- 2/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@@ -387,15 -386,16 +387,19 @@@ public class FeatureRenderer extend
  
      FeaturesFile ffile = new FeaturesFile();
  
-     if (reply == JvOptionPane.OK_OPTION && name.getText().length() > 0)
 -    String enteredType = name.getText().trim();
++    final String enteredType = name.getText().trim();
++    final String enteredGroup = group.getText().trim();
++    final String enteredDescription = description.getText().replaceAll("\n", " ");
++
+     if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
      {
        /*
         * update default values only if creating using default values
         */
        if (useLastDefaults)
        {
-         lastFeatureAdded = name.getText().trim();
-         lastFeatureGroupAdded = group.getText().trim();
+         lastFeatureAdded = enteredType;
 -        lastFeatureGroupAdded = group.getText().trim();
++        lastFeatureGroupAdded = enteredGroup;
          // TODO: determine if the null feature group is valid
          if (lastFeatureGroupAdded.length() < 1)
          {
@@@ -421,52 -421,26 +425,50 @@@
        {
          /*
           * YES_OPTION corresponds to the Amend button
--         * need to refresh Feature Settings if type, group or colour changed
++         * need to refresh Feature Settings if type, group or colour changed;
++         * note we don't force the feature to be visible - the user has been
++         * warned if a hidden feature type or group was entered
           */
-         String newType = name.getText().trim();
-         String newFeatureGroup = group.getText().trim();
-         String newDescription = description.getText().replaceAll("\n", " ");
-         boolean refreshSettings = (!featureType.equals(sf.type) || !featureGroup
-                 .equals(sf.featureGroup));
 -        sf.type = enteredType;
 -        sf.featureGroup = group.getText().trim();
 -        sf.description = description.getText().replaceAll("\n", " ");
 -        boolean refreshSettings = (!featureType.equals(sf.type) || !featureGroup
 -                .equals(sf.featureGroup));
++        boolean refreshSettings = (!featureType.equals(enteredType) || !featureGroup
++                .equals(enteredGroup));
          refreshSettings |= (fcol != oldcol);
-         setColour(newType, fcol);
- /*?*/        getFeaturesDisplayed().setVisible(newType);
 -
 -        setColour(sf.type, fcol);
 -
++        setColour(enteredType, fcol);
 +        int newBegin = sf.begin;
 +        int newEnd = sf.end;
          try
          {
 -          sf.begin = ((Integer) start.getValue()).intValue();
 -          sf.end = ((Integer) end.getValue()).intValue();
 +          newBegin = ((Integer) start.getValue()).intValue();
 +          newEnd = ((Integer) end.getValue()).intValue();
          } catch (NumberFormatException ex)
          {
 +          // JSpinner doesn't accept invalid format data :-)
 +        }
 +
 +        /*
 +         * replace the feature by deleting it and adding a new one
 +         * (to ensure integrity of SequenceFeatures data store)
 +         */
 +        sequences.get(0).deleteFeature(sf);
-         SequenceFeature newSf = new SequenceFeature(newType,
-                 newDescription, newBegin, newEnd, sf.getScore(),
-                 newFeatureGroup);
++        SequenceFeature newSf = new SequenceFeature(enteredType,
++                enteredDescription, newBegin, newEnd, sf.getScore(),
++                enteredGroup);
 +        // ensure any additional properties are copied
 +        if (sf.otherDetails != null)
 +        {
 +          newSf.otherDetails = new HashMap<String, Object>(sf.otherDetails);
 +        }
 +        ffile.parseDescriptionHTML(newSf, false);
 +        // add any additional links not parsed from description
 +        if (sf.links != null)
 +        {
 +          for (String link : sf.links)
 +          {
 +            newSf.addLink(link);
 +          }
          }
 +        // amend features only gets one sequence to act on
 +        sequences.get(0).addSequenceFeature(newSf);
  
 -        ffile.parseDescriptionHTML(sf, false);
          if (refreshSettings)
          {
            featuresAdded();
@@@ -481,15 -455,15 +483,14 @@@
          for (int i = 0; i < sequences.size(); i++)
          {
            SequenceFeature sf = features.get(i);
-           sf.type = name.getText().trim();
-           // fix for JAL-1538 - always set feature group here
-           sf.featureGroup = group.getText().trim();
-           sf.description = description.getText().replaceAll("\n", " ");
-           sequences.get(i).addSequenceFeature(sf);
-           ffile.parseDescriptionHTML(sf, false);
 -          sf.type = enteredType;
 -          // fix for JAL-1538 - always set feature group here
 -          sf.featureGroup = group.getText().trim();
 -          sf.description = description.getText().replaceAll("\n", " ");
 -          sequences.get(i).addSequenceFeature(sf);
 -          ffile.parseDescriptionHTML(sf, false);
++          SequenceFeature sf2 = new SequenceFeature(enteredType,
++                  enteredDescription, sf.getBegin(), sf.getEnd(),
++                  Float.NaN, enteredGroup);
++          sequences.get(i).addSequenceFeature(sf2);
++          ffile.parseDescriptionHTML(sf2, false);
          }
  
-         setColour(lastFeatureAdded, fcol);
+         setColour(enteredType, fcol);
  
          featuresAdded();