Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

diff --combined src/jalview/gui/AlignFrame.java
index 1970388,b646d5b..8462b8d
--- 1/src/jalview/gui/AlignFrame.java
--- 2/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@@ -1098,6 -1098,11 +1098,6 @@@ public class AlignFrame extends GAlignF
                  .lastIndexOf(java.io.File.separatorChar) + 1);
        }
  
 -      /*
 -       * First save any linked Chimera session.
 -       */
 -      Desktop.instance.saveChimeraSessions(file);
 -
        success = new Jalview2XML().saveAlignment(this, file, shortName);
  
        statusBar.setText(MessageManager.formatMessage(
@@@ -1245,11 -1250,13 +1245,13 @@@
          alignmentToExport = viewport.getAlignment();
          alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
                  .getColumnSelection().getHiddenColumns());
+         viewport.setIncludeHiddenRegion(false);
        }
        else
        {
          // export all region including visible
          alignmentToExport = hiddenSeqs.getFullAlignment();
+         viewport.setIncludeHiddenRegion(true);
        }
      }
  
@@@ -6121,13 -6128,17 +6123,17 @@@
    {
      AlignmentI al = viewport.getAlignment();
      HiddenSequences hiddenSeqs = al.getHiddenSequences();
+     boolean hasHiddenRows = false;
      for (SequenceI seq : al.getSequencesArray())
        {
          if (seq.isHidden())
          {
          hiddenSeqs.hideSequence(seq);
+         hasHiddenRows = true;
          }
        }
+     viewport.setHasHiddenRows(hasHiddenRows);
+     firePropertyChange("alignment", null, al.getSequences());
    }
  }