Merge branch 'features/1769_headless-mode-test' into develop

diff --combined src/jalview/gui/AlignFrame.java
index aa41ca9,8144738..68d7397
--- 1/src/jalview/gui/AlignFrame.java
--- 2/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@@ -37,6 -37,7 +37,7 @@@ import jalview.api.SplitContainerI
  import jalview.api.ViewStyleI;
  import jalview.api.analysis.ScoreModelI;
  import jalview.bin.Cache;
+ import jalview.bin.Jalview;
  import jalview.commands.CommandI;
  import jalview.commands.EditCommand;
  import jalview.commands.EditCommand.Action;
@@@ -335,7 -336,10 +336,10 @@@ public class AlignFrame extends GAlignF
     */
    void init()
    {
-     progressBar = new ProgressBar(this.statusPanel, this.statusBar);
+     if (!Jalview.isHeadlessMode())
+     {
+       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
+     }
  
      avc = new jalview.controller.AlignViewController(this, viewport,
              alignPanel);
@@@ -1135,8 -1139,10 +1139,10 @@@
        {
          warningMessage("Cannot save file " + fileName + " using format "
                  + format, "Alignment output format not supported");
-         saveAs_actionPerformed(null);
-         // JBPNote need to have a raise_gui flag here
+         if (!Jalview.isHeadlessMode())
+         {
+           saveAs_actionPerformed(null);
+         }
          return false;
        }
  
@@@ -4855,7 -4861,7 +4861,7 @@@
  
              // temporary flag until SplitFrame is released
              boolean asSplitFrame = Cache.getDefault(
 -                    Preferences.ENABLE_SPLIT_FRAME, false);
 +                    Preferences.ENABLE_SPLIT_FRAME, true);
              if (asSplitFrame)
              {
                /*
@@@ -4987,7 -4993,7 +4993,7 @@@
                "label.translation_of_params", new Object[]
                { this.getTitle() });
        af.setTitle(newTitle);
 -      if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, false))
 +      if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
        {
          final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
          viewport.openSplitFrame(af, new Alignment(seqs),