Merge branch 'features/JAL-1541_BioJsMSA' into develop

diff --combined src/jalview/gui/AlignFrame.java
index 001c2d5,79868f6..9d56224
--- 1/src/jalview/gui/AlignFrame.java
--- 2/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@@ -1342,8 -1342,9 +1342,9 @@@ public class AlignFrame extends GAlignF
    @Override
    public void bioJSMenuItem_actionPerformed(ActionEvent e)
    {
-     new BioJsHTMLOutput(alignPanel,
+     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel,
              alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+     bjs.exportJalviewAlignmentAsBioJsHtmlFile();
    }
    public void createImageMap(File file, String image)
    {
@@@ -5964,13 -5965,6 +5965,13 @@@
      for (AlignmentAnnotation aa : alignPanel.getAlignment()
              .getAlignmentAnnotation())
      {
 +      /*
 +       * don't display non-positional annotations on an alignment
 +       */
 +      if (aa.annotations == null)
 +      {
 +        continue;
 +      }
        boolean apply = (aa.sequenceRef == null && forAlignment)
                || (aa.sequenceRef != null && forSequences);
        if (apply)