Merge branch 'develop' into feature/JAL-3187linkedFeatures

diff --combined src/jalview/project/Jalview2XML.java
index 3efc009,e57dd01..2ce6ea7
--- 1/src/jalview/project/Jalview2XML.java
--- 2/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@@ -58,6 -58,7 +58,6 @@@ import jalview.gui.AlignmentPanel
  import jalview.gui.AppVarna;
  import jalview.gui.ChimeraViewFrame;
  import jalview.gui.Desktop;
 -import jalview.gui.FeatureRenderer;
  import jalview.gui.Jalview2XML_V1;
  import jalview.gui.JvOptionPane;
  import jalview.gui.OOMWarning;
@@@ -91,7 -92,6 +91,7 @@@ import jalview.util.matcher.Condition
  import jalview.viewmodel.AlignmentViewport;
  import jalview.viewmodel.PCAModel;
  import jalview.viewmodel.ViewportRanges;
 +import jalview.viewmodel.seqfeatures.FeatureRendererModel;
  import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
  import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
  import jalview.ws.jws2.Jws2Discoverer;
@@@ -1488,7 -1488,7 +1488,7 @@@ public class Jalview2XM
        {
          FeatureSettings fs = new FeatureSettings();
  
 -        FeatureRenderer fr = ap.getSeqPanel().seqCanvas
 +        FeatureRendererModel fr = ap.getSeqPanel().seqCanvas
                  .getFeatureRenderer();
          String[] renderOrder = fr.getRenderOrder().toArray(new String[0]);
  
@@@ -5007,7 -5007,7 +5007,7 @@@
      // recover feature settings
      if (jm.getFeatureSettings() != null)
      {
 -      FeatureRenderer fr = af.alignPanel.getSeqPanel().seqCanvas
 +      FeatureRendererModel fr = af.alignPanel.getSeqPanel().seqCanvas
                .getFeatureRenderer();
        FeaturesDisplayed fdi;
        viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
@@@ -5829,15 -5829,16 +5829,16 @@@
      jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
              fto, m.getMapFromUnit().intValue(),
              m.getMapToUnit().intValue());
-     // if (m.getMappingChoice() != null)
-     // {
-     // MappingChoice mc = m.getMappingChoice();
+ 
+     /*
+      * (optional) choice of dseqFor or Sequence
+      */
      if (m.getDseqFor() != null)
      {
        String dsfor = m.getDseqFor();
        if (seqRefIds.containsKey(dsfor))
        {
-         /**
+         /*
           * recover from hash
           */
          jmap.setTo(seqRefIds.get(dsfor));
@@@ -5847,9 -5848,9 +5848,9 @@@
          frefedSequence.add(newMappingRef(dsfor, jmap));
        }
      }
-     else
+     else if (m.getSequence() != null)
      {
-       /**
+       /*
         * local sequence definition
         */
        Sequence ms = m.getSequence();