Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport

diff --combined src/jalview/controller/AlignViewController.java
index 151af0e,6a7e222..be84bbf
--- 1/src/jalview/controller/AlignViewController.java
--- 2/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@@ -333,20 -333,20 +333,20 @@@ public class AlignViewController implem
      gps = fr == null ? null : fr.getDisplayedFeatureGroups();
      if (typ != null)
      {
-       ArrayList types = new ArrayList();
-       for (int i = 0; i < typ.length; i++)
+       List<String> types = new ArrayList<String>();
+       for (String displayed : typ)
        {
-         if (typ[i] != null)
+         if (displayed != null)
          {
-           types.add(typ[i]);
+           types.add(displayed);
          }
-         typ = new String[types.size()];
-         types.toArray(typ);
        }
+       typ = new String[types.size()];
+       types.toArray(typ);
      }
      if (gps != null)
      {
-       ArrayList grps = new ArrayList();
+       List<String> grps = new ArrayList<String>();
  
        for (int i = 0; i < gps.length; i++)
        {
@@@ -393,7 -393,7 +393,7 @@@
      boolean featuresFile = false;
      try
      {
 -      featuresFile = new FeaturesFile(file, protocol).parse(viewport
 +      featuresFile = new FeaturesFile(false, file, protocol).parse(viewport
                .getAlignment().getDataset(), alignPanel.getFeatureRenderer()
                .getFeatureColours(), false, relaxedIdMatching);
      } catch (Exception ex)