From: hansonr <hansonr@STO24954W.ad.stolaf.edu>
Date: Tue, 27 Aug 2019 22:02:45 +0000 (-0500)
Subject: JAL-3253-applet headless branch - just experimenting.
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=55f6f8a9ddd0b8bb4445d1cc582297af1d0aa4c5;p=jalview.git

JAL-3253-applet headless branch - just experimenting.

Windows (at least) headless does not allow for JInternalFrame even
though, on paper, JInternalFrame should not be a heavy-weight component.
---

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index fae2b75..2752008 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -292,6 +292,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
     }
     else
     {
+      // BH 2019.08.26 cannot pass null
       System.setSecurityManager(null);
     }
 
@@ -342,6 +343,9 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
               || "true".equals(System.getProperty("java.awt.headless")))
       {
         headless = true;
+
+        System.out.println("Headless operation detected.");
+
       }
 
       // anything else!
@@ -398,7 +402,9 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
 
     try
     {
-      UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+      UIManager.setLookAndFeel(
+              headless ? "javax.swing.plaf.metal.MetalLookAndFeel"
+                      : UIManager.getSystemLookAndFeelClassName());
     } catch (Exception ex)
     {
       System.err.println("Unexpected Look and Feel Exception");
@@ -616,7 +622,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
         {
           if (!(new File(file)).exists())
           {
-            System.out.println("Can't find " + file);
+            System.out.println(
+                    "Can't find " + new File(file).getAbsolutePath());
             if (headless)
             {
               System.exit(1);
@@ -753,7 +760,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
 
         if (aparser.contains(ArgsParser.SHOWOVERVIEW))
         {
-          af.overviewMenuItem_actionPerformed(null);
+          if (!headless)
+          {
+            af.overviewMenuItem_actionPerformed(null);
+          }
           System.out.println("CMD [showoverview] executed successfully!");
         }
 
diff --git a/src/jalview/bin/JalviewAppLoader.java b/src/jalview/bin/JalviewAppLoader.java
index 51a0330..6225155 100644
--- a/src/jalview/bin/JalviewAppLoader.java
+++ b/src/jalview/bin/JalviewAppLoader.java
@@ -987,9 +987,12 @@ public class JalviewAppLoader
           @Override
           public void run()
           {
-            StructureSelectionManager
+            if (Desktop.getInstance() != null)
+            {
+              StructureSelectionManager
                     .getStructureSelectionManager(Desktop.getInstance())
                     .mouseOverVamsasSequence(sq, sq.findIndex(pos), null);
+            }
           }
         });
       }
diff --git a/src/jalview/bin/JalviewJS2.java b/src/jalview/bin/JalviewJS2.java
index 1ed9f27..4a21374 100644
--- a/src/jalview/bin/JalviewJS2.java
+++ b/src/jalview/bin/JalviewJS2.java
@@ -33,10 +33,12 @@ public class JalviewJS2
   {
     if (args.length == 0)
     {
-      args = new String[] { "open", "examples/uniref50.fa", "features",
+      args = new String[] { "headless", "open", "examples/uniref50.fa",
+          "features",
           "examples/exampleFeatures.txt"
           , "noannotation"
           , "showoverview"
+          , "png", "ALIGN.png"
       };
     }
     Jalview.main(args);
diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java
index 475167f..cb2b8cc 100644
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -74,7 +74,7 @@ public class SequenceFeatures implements SequenceFeaturesI
    */
   private final int INTERVAL_STORE_MODE = (
   // true || //
-  true || Platform.isJS() ? //
+  Platform.isJS() ? //
           INTERVAL_STORE_LINKED_LIST //
           : INTERVAL_STORE_NCLIST//
   );
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index bac06e9..d73d893 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -131,6 +131,7 @@ import java.awt.event.MouseEvent;
 import java.awt.print.PageFormat;
 import java.awt.print.PrinterJob;
 import java.beans.PropertyChangeEvent;
+import java.beans.PropertyVetoException;
 import java.io.File;
 import java.io.FileWriter;
 import java.io.PrintWriter;
@@ -170,6 +171,17 @@ public class AlignFrame extends GAlignFrame
         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 {
 
+  public class IFrame extends JInternalFrame
+  {
+    public AlignFrame alignframe;
+
+    IFrame(AlignFrame alignframe)
+    {
+      this.alignframe = alignframe;
+    }
+
+  }
+
   public static final int DEFAULT_WIDTH = 700;
 
   public static final int DEFAULT_HEIGHT = 500;
@@ -291,15 +303,25 @@ public class AlignFrame extends GAlignFrame
   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
           int height, String sequenceSetId, String viewId)
   {
+    super();
+
+    System.out.println("AlignFrame 1");
+
     setSize(width, height);
 
+    System.out.println("GAlignFrame 2");
+
     if (al.getDataset() == null)
     {
       al.setDataset(null);
     }
 
+    System.out.println("GAlignFrame 3");
+
     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 
+    System.out.println("GAlignFrame 4");
+
     init();
   }
 
@@ -343,8 +365,12 @@ public class AlignFrame extends GAlignFrame
    */
   void init()
   {
+
+    System.out.println("AlignFrame 8");
     boolean newPanel = (alignPanel == null);
     viewport.setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+
+    System.out.println("AlignFrame 9");
     if (newPanel)
     {
       if (Platform.isJS())
@@ -360,9 +386,13 @@ public class AlignFrame extends GAlignFrame
         boolean showAnnotation = Jalview.getInstance().getShowAnnotation();
         viewport.setShowAnnotation(showAnnotation);
       }
+      System.out.println("AlignFrame 11");
       alignPanel = new AlignmentPanel(this, viewport);
+      System.out.println("GAlignFrame 12");
     }
+    System.out.println("GAlignFrame 13");
     addAlignmentPanel(alignPanel, newPanel);
+    System.out.println("GAlignFrame 14");
 
     // setBackground(Color.white); // BH 2019
 	  	  
@@ -782,11 +812,14 @@ public class AlignFrame extends GAlignFrame
 
     int aSize = alignPanels.size();
 
+    System.out.println("AlignFrame 21");
+
     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 
+    System.out.println("AlignFrame 23");
     if (aSize == 1 && ap.av.getViewName() == null)
     {
-      this.getContentPane().add(ap, BorderLayout.CENTER);
+      getContentPane().add(ap, BorderLayout.CENTER);
     }
     else
     {
@@ -824,9 +857,10 @@ public class AlignFrame extends GAlignFrame
     tabbedPane.setVisible(true);
     AlignmentPanel first = alignPanels.get(0);
     tabbedPane.addTab(first.av.getViewName(), first);
-    this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
+    getContentPane().add(tabbedPane, BorderLayout.CENTER);
   }
 
+
   public AlignViewport getViewport()
   {
     return viewport;
@@ -858,7 +892,8 @@ public class AlignFrame extends GAlignFrame
                 }
               }
             });
-    addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+    iframe.addInternalFrameListener(
+            new javax.swing.event.InternalFrameAdapter()
     {
       @Override
       public void internalFrameClosed(
@@ -1058,12 +1093,12 @@ public class AlignFrame extends GAlignFrame
       // file is reloaded.
       if (FileFormat.Jalview.equals(currentFileFormat))
       {
-        JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
+        AlignFrame[] frames = Desktop.getAlignFrames();
         for (int i = 0; i < frames.length; i++)
         {
           if (frames[i] instanceof AlignFrame && frames[i] != this
-                  && ((AlignFrame) frames[i]).fileName != null
-                  && ((AlignFrame) frames[i]).fileName.equals(fileName))
+                  && frames[i].fileName != null
+                  && frames[i].fileName.equals(fileName))
           {
             try
             {
@@ -1077,7 +1112,7 @@ public class AlignFrame extends GAlignFrame
         }
         Desktop.getInstance().closeAssociatedWindows();
 
-        FileLoader loader = new FileLoader();
+        FileLoader loader = new FileLoader(!Jalview.isHeadlessMode());
         DataSourceType protocol = fileName.startsWith("http:")
                 ? DataSourceType.URL
                 : DataSourceType.FILE;
@@ -1130,6 +1165,7 @@ public class AlignFrame extends GAlignFrame
     }
   }
 
+
   @Override
   public void addFromText_actionPerformed(ActionEvent e)
   {
@@ -1255,7 +1291,7 @@ public class AlignFrame extends GAlignFrame
 
     if (FileFormat.Jalview.equals(format))
     {
-      String shortName = title;
+      String shortName = getTitle();
       if (shortName.indexOf(File.separatorChar) > -1)
       {
         shortName = shortName.substring(
@@ -1544,7 +1580,7 @@ public class AlignFrame extends GAlignFrame
       {
         if (closeAllTabs)
         {
-          if (this.isClosed())
+          if (isClosed())
           {
             // really close all the windows - otherwise wait till
             // setClosed(true) is called
@@ -1567,7 +1603,7 @@ public class AlignFrame extends GAlignFrame
          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
          * be called recursively, with the frame now in 'closed' state
          */
-        this.setClosed(true);
+        iframe.setClosed(true);
       }
     } catch (Exception ex)
     {
@@ -2319,13 +2355,13 @@ public class AlignFrame extends GAlignFrame
         // title a concatenation of operations.
         if (!externalPaste)
         {
-          if (title.startsWith("Copied sequences"))
+          if (getTitle().startsWith("Copied sequences"))
           {
-            newtitle = title;
+            newtitle = getTitle();
           }
           else
           {
-            newtitle = newtitle.concat("- from " + title);
+            newtitle = newtitle.concat("- from " + getTitle());
           }
         }
         else
@@ -2375,17 +2411,18 @@ public class AlignFrame extends GAlignFrame
       // TODO: maintain provenance of an alignment, rather than just make the
       // title a concatenation of operations.
       {
-        if (title.startsWith("Copied sequences"))
+        if (getTitle().startsWith("Copied sequences"))
         {
-          newtitle = title;
+          newtitle = getTitle();
         }
         else
         {
-          newtitle = newtitle.concat("- from " + title);
+          newtitle = newtitle.concat("- from " + getTitle());
         }
       }
 
-      Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
+      Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
+              DEFAULT_HEIGHT);
 
     } catch (Exception ex)
     {
@@ -2444,7 +2481,7 @@ public class AlignFrame extends GAlignFrame
 		    {
 		      try
 		      {
-		        AlignFrame.this.setClosed(true);
+            AlignFrame.this.getIFrame().setClosed(true);
 		      } catch (Exception ex)
 		      {
 		      }
@@ -3773,7 +3810,7 @@ public class AlignFrame extends GAlignFrame
       frameTitle += viewport.getViewName() + " of ";
     }
 
-    frameTitle += this.title;
+    frameTitle += this.getTitle();
 
     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
   }
@@ -4850,7 +4887,7 @@ public class AlignFrame extends GAlignFrame
           }
           else
           {
-            new FileLoader().loadFile(viewport, file, sourceType, format);
+            new FileLoader(!Jalview.isHeadlessMode()).loadFile(viewport, file, sourceType, format);
           }
         }
       }
@@ -5660,12 +5697,13 @@ public class AlignFrame extends GAlignFrame
     }
     AlignmentI cdna = new Alignment(
             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
-    GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
+    AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
             AlignFrame.DEFAULT_HEIGHT);
     cdna.alignAs(alignment);
     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
-            + this.title;
-    Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
+            + getTitle();
+    Desktop.addInternalFrame(alignFrame, newtitle,
+            AlignFrame.DEFAULT_WIDTH,
             AlignFrame.DEFAULT_HEIGHT);
   }
 
@@ -5899,6 +5937,41 @@ public class AlignFrame extends GAlignFrame
     alignPanel.getSeqPanel().selection(sel, csel, hidden, null);
   }
 
+  public void setSelected(boolean b) throws PropertyVetoException
+  {
+    if (iframe != null)
+    {
+      iframe.setSelected(b);
+    }
+  }
+
+  @Override
+  protected JInternalFrame getInternalFrame()
+  {
+    return new IFrame(this);
+  }
+
+  public void dispose()
+  {
+    if (iframe != null)
+    {
+      iframe.dispose();
+    }
+  }
+
+  public void setMaximum(boolean b) throws PropertyVetoException
+  {
+    if (iframe != null)
+    {
+      iframe.setMaximum(b);
+    }
+  }
+
+  public boolean isClosed()
+  {
+    return (iframe != null && iframe.isClosed());
+  }
+
 }
 
 class PrintThread extends Thread
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index eb9c180..779b48e 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -391,7 +391,7 @@ public class AlignViewport extends AlignmentViewport
      */
     if (align != null)
     {
-      Desktop.getInstance().getStructureSelectionManager()
+      getStructureSelectionManager()
               .registerMappings(align.getCodonFrames());
     }
 
@@ -410,10 +410,13 @@ public class AlignViewport extends AlignmentViewport
     if (al != null)
     {
       List<AlignedCodonFrame> mappings = al.getCodonFrames();
-      if (mappings != null)
+      if (mappings != null && Desktop.getInstance() != null)
       {
-        StructureSelectionManager ssm = Desktop.getInstance()
-                .getStructureSelectionManager();
+        // StructureSelectionManager ssm = Desktop.getInstance()
+        // .getStructureSelectionManager();
+
+        // BH 2019.08.27 allows for null Desktop instance
+        StructureSelectionManager ssm = getStructureSelectionManager();
         for (AlignedCodonFrame acf : mappings)
         {
           if (noReferencesTo(acf))
@@ -538,7 +541,7 @@ public class AlignViewport extends AlignmentViewport
   @Override
   public void sendSelection()
   {
-    Desktop.getInstance().getStructureSelectionManager().sendSelection(
+    getStructureSelectionManager().sendSelection(
             new SequenceGroup(getSelectionGroup()),
             new ColumnSelection(getColumnSelection()),
             new HiddenColumns(getAlignment().getHiddenColumns()), this);
@@ -582,7 +585,9 @@ public class AlignViewport extends AlignmentViewport
   @Override
   public StructureSelectionManager getStructureSelectionManager()
   {
-    return Desktop.getInstance().getStructureSelectionManager();
+    // BH allows for null Desktop instance
+    return StructureSelectionManager
+            .getStructureSelectionManager(Desktop.getInstance());
   }
 
   @Override
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index b636fa7..3bb0259 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -126,15 +126,24 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
+
+    System.out.println("AP 1");
     setBackground(Color.white); // BH 2019
     setOpaque(true);
     alignFrame = af;
     this.av = av;
+
+    System.out.println("AP 2");
     setSeqPanel(new SeqPanel(av, this));
+
+    System.out.println("AP 3");
     setIdPanel(new IdPanel(av, this));
 
+    System.out.println("AP 4");
+
     setScalePanel(new ScalePanel(av, this));
 
+    System.out.println("AP 5");
     idPanelHolder.add(getIdPanel(), BorderLayout.CENTER);
     idwidthAdjuster = new IdwidthAdjuster(this);
     idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
@@ -254,7 +263,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
     getIdPanel().getIdCanvas().setPreferredSize(d);
     hscrollFillerPanel.setPreferredSize(d);
 
+    System.out.println("AP 99");
     repaint();
+
+    System.out.println("AP 100");
   }
 
   /**
diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index b81c344..acc1394 100644
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -24,6 +24,7 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
+import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 
 /**
@@ -61,7 +62,8 @@ public class AssociatePdbFileWithSeq
   {
     PDBEntry entry = new PDBEntry();
     StructureFile pdbfile = null;
-    pdbfile = Desktop.getInstance().getStructureSelectionManager()
+    pdbfile = StructureSelectionManager
+            .getStructureSelectionManager(Desktop.getInstance())
             .setMapping(false, new SequenceI[]
             { sequence }, null, fileName, type);
     if (pdbfile == null)
diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java
index 2ee741b..0910843 100644
--- a/src/jalview/gui/CrossRefAction.java
+++ b/src/jalview/gui/CrossRefAction.java
@@ -34,6 +34,7 @@ import jalview.datamodel.SequenceI;
 import jalview.ext.ensembl.EnsemblInfo;
 import jalview.ext.ensembl.EnsemblMap;
 import jalview.io.gff.SequenceOntologyI;
+import jalview.structure.StructureSelectionManager;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
@@ -440,7 +441,8 @@ public class CrossRefAction implements Runnable
      * register any new mappings for sequence mouseover etc
      * (will not duplicate any previously registered mappings)
      */
-    Desktop.getInstance().getStructureSelectionManager()
+    StructureSelectionManager
+            .getStructureSelectionManager(Desktop.getInstance())
             .registerMappings(dataset.getCodonFrames());
 
     if (copyAlignment.getHeight() <= 0)
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index a58e22a..d312a25 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -199,7 +199,7 @@ public class Desktop extends GDesktop
 
   public static MyDesktopPane getDesktopPane()
   {
-    Desktop desktop = Desktop.getInstance();
+    Desktop desktop = getInstance();
     return desktop == null ? null : desktop.desktopPane;
   }
 
@@ -799,7 +799,7 @@ public class Desktop extends GDesktop
         FileFormatI format = new IdentifyFile().identify(file,
                 DataSourceType.PASTE);
 
-        new FileLoader().loadFile(file, DataSourceType.PASTE, format);
+        new FileLoader(true).loadFile(file, DataSourceType.PASTE, format);
 
       }
     } catch (Exception ex)
@@ -909,7 +909,7 @@ public class Desktop extends GDesktop
     // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
     // IF JALVIEW IS RUNNING HEADLESS
     // ///////////////////////////////////////////////
-    if (Desktop.getInstance().instanceOnly || Jalview.isHeadlessMode())
+    if (Jalview.isHeadlessMode() || getInstance().instanceOnly)
     {
       return;
     }
@@ -925,7 +925,7 @@ public class Desktop extends GDesktop
       // The Alignment Frame window could be added from a number of places,
       // hence,
       // I did this here in order not to miss out on any Alignment frame.
-      if (frame instanceof AlignFrame)
+      if (frame instanceof AlignFrame.IFrame)
       {
         frame.setMinimumSize(new Dimension(ALIGN_FRAME_DEFAULT_MIN_WIDTH,
                 ALIGN_FRAME_DEFAULT_MIN_HEIGHT));
@@ -958,9 +958,9 @@ public class Desktop extends GDesktop
         JInternalFrame itf = getDesktopPane().getSelectedFrame();
         if (itf != null)
         {
-          if (itf instanceof AlignFrame)
+          if (itf.getContentPane() instanceof AlignFrame)
           {
-            Jalview.setCurrentAlignFrame((AlignFrame) itf);
+            Jalview.setCurrentAlignFrame((AlignFrame) itf.getContentPane());
           }
           itf.requestFocus();
         }
@@ -987,7 +987,7 @@ public class Desktop extends GDesktop
         {
           menuItem.removeActionListener(menuItem.getActionListeners()[0]);
         }
-        Desktop.getInstance().windowMenu.remove(menuItem);
+        getInstance().windowMenu.remove(menuItem);
       }
     });
 
@@ -1011,7 +1011,7 @@ public class Desktop extends GDesktop
 
     getDesktopPane().add(frame);
 
-    Desktop.getInstance().windowMenu.add(menuItem);
+    getInstance().windowMenu.add(menuItem);
 
     frame.toFront();
     try
@@ -1068,7 +1068,7 @@ public class Desktop extends GDesktop
   {
     if (!internalCopy)
     {
-      Desktop.getInstance().jalviewClipboard = null;
+      getInstance().jalviewClipboard = null;
     }
 
     internalCopy = false;
@@ -1636,9 +1636,9 @@ public class Desktop extends GDesktop
     }
 
     AlignmentViewport source = null, target = null;
-    if (frames[0] instanceof AlignFrame)
+    if (frames[0] instanceof AlignFrame.IFrame)
     {
-      source = ((AlignFrame) frames[0]).getCurrentView();
+      source = ((AlignFrame.IFrame) frames[0]).alignframe.getCurrentView();
     }
     else if (frames[0] instanceof TreePanel)
     {
@@ -1662,9 +1662,10 @@ public class Desktop extends GDesktop
         {
           continue;
         }
-        if (frames[i] instanceof AlignFrame)
+        if (frames[i] instanceof AlignFrame.IFrame)
         {
-          target = ((AlignFrame) frames[i]).getCurrentView();
+          target = ((AlignFrame.IFrame) frames[i]).alignframe
+                  .getCurrentView();
         }
         else if (frames[i] instanceof TreePanel)
         {
@@ -2080,7 +2081,8 @@ public class Desktop extends GDesktop
 
       ap.av.setGatherViewsHere(false);
 
-      addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
+      addInternalFrame(newaf, af.getTitle(),
+              AlignFrame.DEFAULT_WIDTH,
               AlignFrame.DEFAULT_HEIGHT);
     }
 
@@ -2106,9 +2108,10 @@ public class Desktop extends GDesktop
 
     for (int t = 0; t < frames.length; t++)
     {
-      if (frames[t] instanceof AlignFrame && frames[t] != source)
+      if (frames[t] instanceof AlignFrame.IFrame
+              && ((AlignFrame.IFrame) frames[t]).alignframe != source)
       {
-        AlignFrame af = (AlignFrame) frames[t];
+        AlignFrame af = ((AlignFrame.IFrame) frames[t]).alignframe;
         boolean gatherThis = false;
         for (int a = 0; a < af.alignPanels.size(); a++)
         {
@@ -2686,6 +2689,7 @@ public class Desktop extends GDesktop
         }
       }
     }
+
   }
 
   /**
@@ -2711,9 +2715,9 @@ public class Desktop extends GDesktop
     // REVERSE ORDER
     for (int i = frames.length - 1; i > -1; i--)
     {
-      if (frames[i] instanceof AlignFrame)
+      if (frames[i].getContentPane() instanceof AlignFrame)
       {
-        avp.add((AlignFrame) frames[i]);
+        avp.add((AlignFrame) frames[i].getContentPane());
       }
       else if (frames[i] instanceof SplitFrame)
       {
@@ -3160,7 +3164,7 @@ public class Desktop extends GDesktop
    */
   public static void showUrl(final String url)
   {
-    showUrl(url, Desktop.getInstance());
+    showUrl(url, getInstance());
   }
 
   /**
@@ -3209,7 +3213,7 @@ public class Desktop extends GDesktop
 
   public static ParamManager getUserParameterStore()
   {
-    Desktop d = Desktop.getInstance();
+    Desktop d = getInstance();
     if (d.wsparamManager == null)
     {
       d.wsparamManager = new WsParamSetManager();
@@ -3500,7 +3504,7 @@ public class Desktop extends GDesktop
 
   public static groovy.ui.Console getGroovyConsole()
   {
-    Desktop desktop = Desktop.getInstance();
+    Desktop desktop = getInstance();
     return desktop == null ? null : desktop.groovyConsole;
   }
 
@@ -3773,4 +3777,10 @@ public class Desktop extends GDesktop
     return result;
   }
 
+  public static void addInternalFrame(AlignFrame af, String title,
+          int width, int height)
+  {
+    addInternalFrame(af.getIFrame(), title, width, height);
+  }
+
 }
diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 2a6adda..1ff2dff 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -187,15 +187,14 @@ public class Finder extends GFinder
     }
     // now checks further down the window stack to fix bug
     // https://mantis.lifesci.dundee.ac.uk/view.php?id=36008
-    JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
+    AlignFrame[] frames = Desktop.getAlignFrames();
     for (int f = 0; f < frames.length; f++)
     {
-      JInternalFrame alignFrame = frames[f];
-      if (alignFrame != null && alignFrame instanceof AlignFrame
-              && !alignFrame.isIcon())
+      AlignFrame alignFrame = frames[f];
+      if (alignFrame != null && !alignFrame.getIFrame().isIcon())
       {
-        av = ((AlignFrame) alignFrame).viewport;
-        ap = ((AlignFrame) alignFrame).alignPanel;
+        av = alignFrame.viewport;
+        ap = alignFrame.alignPanel;
         return true;
       }
     }
diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index 4404a8d..6ac37a7 100644
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -43,8 +43,6 @@ import java.util.Hashtable;
 import java.util.IdentityHashMap;
 import java.util.Iterator;
 
-import javax.swing.JInternalFrame;
-
 import uk.ac.vamsas.client.ClientHandle;
 import uk.ac.vamsas.client.IClient;
 import uk.ac.vamsas.client.IClientDocument;
@@ -286,7 +284,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
    */
   protected void updateJalviewGui()
   {
-    JInternalFrame[] frames = jdesktop.getAllFrames();
+    AlignFrame[] frames = Desktop.getAlignFrames();
 
     if (frames == null)
     {
@@ -298,11 +296,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
       // REVERSE ORDER
       for (int i = frames.length - 1; i > -1; i--)
       {
-        if (frames[i] instanceof AlignFrame)
-        {
-          AlignFrame af = (AlignFrame) frames[i];
-          af.alignPanel.alignmentChanged();
-        }
+        frames[i].alignPanel.alignmentChanged();
       }
     } catch (Exception e)
     {
@@ -455,7 +449,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
     VamsasAppDatastore vds = new VamsasAppDatastore(doc, vobj2jv, jv2vobj,
             baseProvEntry(), alRedoState);
     // wander through frames
-    JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
+    AlignFrame[] frames = Desktop.getAlignFrames();
 
     if (frames == null)
     {
@@ -469,9 +463,8 @@ public class VamsasApplication implements SelectionSource, VamsasSource
       // REVERSE ORDER
       for (int i = frames.length - 1; i > -1; i--)
       {
-        if (frames[i] instanceof AlignFrame)
-        {
-          AlignFrame af = (AlignFrame) frames[i];
+
+        AlignFrame af = frames[i];
           if (!viewset.containsKey(af.getViewport().getSequenceSetId()))
           {
             // update alignment and root from frame.
@@ -503,7 +496,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
               viewset.put(af.getViewport().getSequenceSetId(), af);
             }
           }
-        }
+
       }
       // REVERSE ORDER
       // for (int i = frames.length - 1; i > -1; i--)
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index c3afe1f..b41073c 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -37,6 +37,7 @@ import jalview.gui.JvOptionPane;
 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.project.Jalview2XML;
 import jalview.schemes.ColourSchemeI;
+import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.utils.UrlDownloadClient;
@@ -280,6 +281,8 @@ public class FileLoader implements Runnable
   @Override
   public void run()
   {
+
+
     String title = protocol == DataSourceType.PASTE
             ? "Copied From Clipboard"
             : file;
@@ -298,7 +301,8 @@ public class FileLoader implements Runnable
           format = new IdentifyFile().identify(source, false);
           // identify stream and rewind rather than close
         }
-        else if (selectedFile != null) {
+        else if (selectedFile != null)
+        {
           format = new IdentifyFile().identify(selectedFile, protocol);
         }
         else
@@ -324,9 +328,11 @@ public class FileLoader implements Runnable
         }
         return;
       }
+
       // TODO: cache any stream datasources as a temporary file (eg. PDBs
       // retrieved via URL)
-      if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage())
+      if (Desktop.getDesktopPane() != null
+              && Desktop.getDesktopPane().isShowMemoryUsage())
       {
         System.gc();
         memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free
@@ -348,7 +354,8 @@ public class FileLoader implements Runnable
         }
         // BH 2018 switch to File object here instead of filename
         Platform.timeCheck(null, Platform.TIME_MARK);
-        alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(selectedFile == null ? file : selectedFile);
+        alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(
+                selectedFile == null ? file : selectedFile);
         Platform.timeCheck("JVP loaded", Platform.TIME_MARK);
 
       }
@@ -378,27 +385,29 @@ public class FileLoader implements Runnable
                       file.lastIndexOf("."));
               String tempStructureFileStr = createNamedJvTempFile(
                       urlLeafName, structExt);
-              
+
               // BH - switching to File object here so as to hold
               // .秘bytes array directly
               File tempFile = new File(tempStructureFileStr);
               UrlDownloadClient.download(file, tempFile);
-              
-              al = fa.readFile(tempFile, DataSourceType.FILE,
-                      format);
+
+              al = fa.readFile(tempFile, DataSourceType.FILE, format);
               source = fa.getAlignFile();
             }
             else
             {
-              if (selectedFile == null) {
+              if (selectedFile == null)
+              {
                 al = fa.readFile(file, protocol, format);
-                
-              } else {
+
+              }
+              else
+              {
                 al = fa.readFile(selectedFile, protocol, format);
-                             }
+              }
               source = fa.getAlignFile(); // keep reference for later if
-              
-                                          // necessary.
+
+              // necessary.
             }
           }
         } catch (java.io.IOException ex)
@@ -406,9 +415,17 @@ public class FileLoader implements Runnable
           error = ex.getMessage();
         }
 
+        System.out.println("OK1");
+
+
         if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence())
         {
+
+
           // construct and register dataset sequences
+
+          StructureSelectionManager ssm = StructureSelectionManager
+                  .getStructureSelectionManager(Desktop.getInstance());
           for (SequenceI sq : al.getSequences())
           {
             while (sq.getDatasetSequence() != null)
@@ -421,16 +438,17 @@ public class FileLoader implements Runnable
               {
                 // register PDB entries with desktop's structure selection
                 // manager
-                Desktop.getInstance().getStructureSelectionManager()
-                        .registerPDBEntry(pdbe);
+                ssm.registerPDBEntry(pdbe);
               }
             }
           }
 
           FeatureSettingsModelI proxyColourScheme = source
                   .getFeatureColourScheme();
+
           if (viewport != null)
           {
+
             if (proxyColourScheme != null)
             {
               viewport.applyFeaturesStyle(proxyColourScheme);
@@ -440,6 +458,8 @@ public class FileLoader implements Runnable
           }
           else
           {
+
+            System.out.println("OK9");
             // otherwise construct the alignFrame
 
             if (source instanceof ComplexAlignFile)
@@ -452,8 +472,10 @@ public class FileLoader implements Runnable
                       .getGlobalColourScheme();
               FeaturesDisplayedI fd = ((ComplexAlignFile) source)
                       .getDisplayedFeatures();
+
               alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
                       AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+
               alignFrame.getViewport().setFeaturesDisplayed(fd);
               alignFrame.getViewport().setShowSequenceFeatures(
                       ((ComplexAlignFile) source).isShowSeqFeatures());
@@ -466,28 +488,64 @@ public class FileLoader implements Runnable
             }
             else
             {
-              alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
-                      AlignFrame.DEFAULT_HEIGHT);
+
+              // Headless start fails here in Windows
+
+              // Sorry, no JInternalFrame when headless, at least in Windows.
+              // Not clear why that would be, since an InternalFrame is not a
+              // top-level component. But maybe it is
+
+              System.out.println("FileLoader test1");
+
+              try
+              {
+                //
+                alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+                        AlignFrame.DEFAULT_HEIGHT);
+
+                System.out.println("FileLoader test2");
+
+              } catch (Throwable t)
+              {
+                System.out.println(t);
+                t.printStackTrace();
+              }
+
               if (source instanceof FeaturesSourceI)
               {
+
+                System.out.println("FileLoader test3");
+
                 alignFrame.getViewport().setShowSequenceFeatures(true);
               }
             }
             // add metadata and update ui
+
+            System.out.println("FileLoader test4");
+
             if (!(protocol == DataSourceType.PASTE))
             {
+
+              System.out.println("FileLoader test5");
               alignFrame.setFileName(file, format);
               alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS
             }
+
+            System.out.println("FileLoader test6");
+
             if (proxyColourScheme != null)
             {
               alignFrame.getViewport()
                       .applyFeaturesStyle(proxyColourScheme);
             }
+
+            System.out.println("FileLoader test7");
+
             alignFrame.setStatus(MessageManager.formatMessage(
                     "label.successfully_loaded_file", new String[]
                     { title }));
 
+            System.out.println("FileLoader test8" + raiseGUI);
             if (raiseGUI)
             {
               // add the window to the GUI
@@ -510,6 +568,9 @@ public class FileLoader implements Runnable
         }
         else
         {
+
+          System.out.println("OK10");
+
           if (Desktop.getInstance() != null)
           {
             Desktop.getInstance().stopLoading();
@@ -519,15 +580,15 @@ public class FileLoader implements Runnable
                   "label.couldnt_load_file") + " " + title + "\n" + error;
           // TODO: refactor FileLoader to be independent of Desktop / Applet GUI
           // bits ?
-          if (raiseGUI && Desktop.getDesktopPane() != null)
+          if (raiseGUI)
           {
             javax.swing.SwingUtilities.invokeLater(new Runnable()
             {
               @Override
               public void run()
               {
-                JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
-                        errorMessage,
+                JvOptionPane.showInternalMessageDialog(
+                        Desktop.getDesktopPane(), errorMessage,
                         MessageManager
                                 .getString("label.error_loading_file"),
                         JvOptionPane.WARNING_MESSAGE);
@@ -541,6 +602,7 @@ public class FileLoader implements Runnable
         }
       }
 
+
       updateRecentlyOpened();
 
     } catch (Exception er)
@@ -589,6 +651,7 @@ public class FileLoader implements Runnable
 
     }
     loadtime += System.currentTimeMillis();
+
     // TODO: Estimate percentage of memory used by a newly loaded alignment -
     // warn if more memory will be needed to work with it
     // System.gc();
@@ -598,7 +661,8 @@ public class FileLoader implements Runnable
     // memory
     // after
     // load
-    if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage())
+    if (Desktop.getDesktopPane() != null
+            && Desktop.getDesktopPane().isShowMemoryUsage())
     {
       if (alignFrame != null)
       {
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 9de31ab..9fc62db 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -35,6 +35,7 @@ import jalview.util.Platform;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
+import java.awt.Container;
 import java.awt.GridLayout;
 import java.awt.Toolkit;
 import java.awt.event.ActionEvent;
@@ -64,8 +65,19 @@ import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
 @SuppressWarnings("serial")
-public class GAlignFrame extends JInternalFrame
+public abstract class GAlignFrame extends JPanel
 {
+
+ 
+  protected abstract JInternalFrame getInternalFrame();
+
+  protected JInternalFrame iframe;
+
+  public JInternalFrame getIFrame()
+  {
+    return iframe;
+  }
+
   protected JMenuBar alignFrameMenuBar = new JMenuBar();
 
   protected JMenuItem closeMenuItem = new JMenuItem();
@@ -218,47 +230,60 @@ public class GAlignFrame extends JInternalFrame
 
   public GAlignFrame()
   {
-    try
-    {
 
-      // for Web-page embedding using id=align-frame-div
-      setName(Jalview.getAppID("alignment"));
+    System.out.println("GAlignFrame init");
 
-      jbInit();
-      setJMenuBar(alignFrameMenuBar);
+    // for Web-page embedding using id=align-frame-div
+    setName(Jalview.getAppID("alignment"));
 
-      // dynamically fill save as menu with available formats
-      for (String ff : FileFormats.getInstance().getWritableFormats(true))
+    try
+    {
+      if (Jalview.isHeadlessMode())
+      {
+        jbInit();
+      }
+      else
       {
-        JMenuItem item = new JMenuItem(ff);
 
-        item.addActionListener(new ActionListener()
+        iframe = getInternalFrame();
+        jbInit();
+        iframe.setJMenuBar(alignFrameMenuBar);
+        // dynamically fill save as menu with available formats
+        for (String ff : FileFormats.getInstance().getWritableFormats(true))
         {
-          @Override
-          public void actionPerformed(ActionEvent e)
+          JMenuItem item = new JMenuItem(ff);
+
+          item.addActionListener(new ActionListener()
           {
-            outputText_actionPerformed(e.getActionCommand());
+            @Override
+            public void actionPerformed(ActionEvent e)
+            {
+              outputText_actionPerformed(e.getActionCommand());
+            }
+          });
+
+          outputTextboxMenu.add(item);
+
+          if (Platform.allowMnemonics()) // was "not mac and not JS"
+          {
+            closeMenuItem.setMnemonic('C');
+            outputTextboxMenu.setMnemonic('T');
+            undoMenuItem.setMnemonic('Z');
+            redoMenuItem.setMnemonic('0');
+            copy.setMnemonic('C');
+            cut.setMnemonic('U');
+            pasteMenu.setMnemonic('P');
+            reload.setMnemonic('R');
           }
-        });
 
-        outputTextboxMenu.add(item);
+        }
+
       }
     } catch (Exception e)
     {
       System.err.println(e.toString());
     }
 
-    if (Platform.allowMnemonics()) // was "not mac and not JS"
-    {
-      closeMenuItem.setMnemonic('C');
-      outputTextboxMenu.setMnemonic('T');
-      undoMenuItem.setMnemonic('Z');
-      redoMenuItem.setMnemonic('0');
-      copy.setMnemonic('C');
-      cut.setMnemonic('U');
-      pasteMenu.setMnemonic('P');
-      reload.setMnemonic('R');
-    }
   }
 
   private void jbInit() throws Exception
@@ -542,8 +567,9 @@ public class GAlignFrame extends JInternalFrame
         pairwiseAlignmentMenuItem_actionPerformed(e);
       }
     });
+    
 
-    this.getContentPane().setLayout(new BorderLayout());
+    getContentPane().setLayout(new BorderLayout());
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
     // statusBar.setBackground(Color.white); BH 2019.08.01 -- this does nothing,
     // as the label is not opaque
@@ -1887,9 +1913,9 @@ public class GAlignFrame extends JInternalFrame
     addSequenceMenu.add(addFromFile);
     addSequenceMenu.add(addFromText);
     addSequenceMenu.add(addFromURL);
-    this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
+    getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
     statusPanel.add(statusBar, null);
-    this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
+    getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
 
     formatMenu.add(font);
     formatMenu.addSeparator();
@@ -2722,4 +2748,33 @@ public class GAlignFrame extends JInternalFrame
   protected void showComplement_actionPerformed(boolean complement)
   {
   }
+
+  private JPanel headlessContentPane;
+
+  protected Container getContentPane()
+  {
+    if (iframe != null)
+    {
+      return iframe.getContentPane();
+    }
+    return (headlessContentPane == null
+            ? (headlessContentPane = new JPanel())
+            : headlessContentPane);
+  }
+
+  private String myTitle;
+
+  public void setTitle(String title)
+  {
+    myTitle = title;
+    if (iframe != null)
+    {
+      iframe.setTitle(title);
+    }
+  }
+
+  public String getTitle()
+  {
+    return myTitle;
+  }
 }
diff --git a/src/jalview/jbgui/GAlignmentPanel.java b/src/jalview/jbgui/GAlignmentPanel.java
index 3dd0205..7cf05de 100755
--- a/src/jalview/jbgui/GAlignmentPanel.java
+++ b/src/jalview/jbgui/GAlignmentPanel.java
@@ -20,45 +20,49 @@
  */
 package jalview.jbgui;
 
+import jalview.bin.Jalview;
+
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Dimension;
 
 import javax.swing.BorderFactory;
 import javax.swing.ButtonGroup;
+import javax.swing.JComponent;
 import javax.swing.JPanel;
 import javax.swing.JScrollBar;
 import javax.swing.JScrollPane;
 import javax.swing.border.Border;
+import javax.swing.plaf.ScrollBarUI;
 
 @SuppressWarnings("serial")
 public class GAlignmentPanel extends JPanel
 {
-	  protected JScrollBar vscroll = new JScrollBar();
+  protected JScrollBar vscroll;// = new JScrollBar();
 
-	  protected JScrollBar hscroll = new JScrollBar();
+  protected JScrollBar hscroll;// = new JScrollBar();
 
-	  BorderLayout borderLayout1 = new BorderLayout();
+  BorderLayout borderLayout1;// = new BorderLayout();
 
-	  BorderLayout borderLayout3 = new BorderLayout();
+  BorderLayout borderLayout3;// = new BorderLayout();
 
-	  BorderLayout borderLayout5 = new BorderLayout();
+  BorderLayout borderLayout5;// = new BorderLayout();
 
-	  BorderLayout borderLayout6 = new BorderLayout();
+  BorderLayout borderLayout6;// = new BorderLayout();
 
-	  ButtonGroup buttonGroup1 = new ButtonGroup();
+  ButtonGroup buttonGroup1;// = new ButtonGroup();
 
-	  BorderLayout borderLayout7 = new BorderLayout();
+  BorderLayout borderLayout7;// = new BorderLayout();
 
-	  BorderLayout borderLayout10 = new BorderLayout();
+  BorderLayout borderLayout10;// = new BorderLayout();
 
-	  BorderLayout borderLayout11 = new BorderLayout();
+  BorderLayout borderLayout11;// = new BorderLayout();
 
-  public JScrollPane annotationScroller = new JScrollPane();
+  public JScrollPane annotationScroller;// = new JScrollPane();
 
 	  Border border1;
 
-	  BorderLayout borderLayout4 = new BorderLayout();
+  BorderLayout borderLayout4;// = new BorderLayout();
 
 	  
 	  static JPanel newJPanel() {  // BH 2019
@@ -70,28 +74,159 @@ public class GAlignmentPanel extends JPanel
 			return p;
 	  }
 
-  protected JPanel sequenceHolderPanel = newJPanel();
-  protected JPanel seqPanelHolder = newJPanel();
-  protected JPanel scalePanelHolder = newJPanel();
-  protected JPanel idPanelHolder = newJPanel();
-  protected JPanel idSpaceFillerPanel1 = newJPanel();
-  public JPanel annotationSpaceFillerHolder = newJPanel();
-  protected JPanel hscrollFillerPanel = newJPanel();
-  JPanel hscrollHolder = newJPanel();
+  static
+  {
+    System.out.println("GAP 1 static ");
+  }
+
+  protected JPanel sequenceHolderPanel;// = new JPanel();
+
+  protected JPanel seqPanelHolder;// = new JPanel();
+
+  protected JPanel scalePanelHolder;// = new JPanel();
+
+  protected JPanel idPanelHolder;// = new JPanel();
+
+  protected JPanel idSpaceFillerPanel1;// = new JPanel();
 
+  public JPanel annotationSpaceFillerHolder;// = new JPanel();
+
+  protected JPanel hscrollFillerPanel;// = new JPanel();
+
+  JPanel hscrollHolder;// = new JPanel();
+
+  static
+  {
+    System.out.println("GAP 2 static ");
+  }
 
 
   public GAlignmentPanel()
   {
+
+    System.out.println("GAP 3a");
+
+    System.out.println(Jalview.isHeadlessMode());
+
     try
     {
+      vscroll = newScrollBar();
+    } catch (Throwable t)
+    {
+      t.printStackTrace();
+      System.exit(1);
+    }
+
+    hscroll = newScrollBar();
+
+    System.out.println("GAP 3b");
+
+    borderLayout1 = new BorderLayout();
+
+    borderLayout3 = new BorderLayout();
+
+    borderLayout5 = new BorderLayout();
+
+    borderLayout6 = new BorderLayout();
+
+    buttonGroup1 = new ButtonGroup();
+
+    borderLayout7 = new BorderLayout();
+
+    borderLayout10 = new BorderLayout();
+
+    borderLayout11 = new BorderLayout();
+
+    System.out.println("GAP 3c");
+    annotationScroller = new JScrollPane() {
+      
+      @Override
+      public void updateUI() { 
+        System.out.println("JScrollPane updateUI");
+      }
+
+      @Override
+      public JScrollBar createVerticalScrollBar()
+      {
+        return newScrollBar();
+      }
+
+      @Override
+      public JScrollBar createHorizontalScrollBar()
+      {
+        return newScrollBar();
+      }
+      
+
+    };
+    System.out.println("GAP 3d");
+
+    borderLayout4 = new BorderLayout();
+
+    System.out.println("GAP 3e");
+    sequenceHolderPanel = newJPanel();
+
+    seqPanelHolder = newJPanel();
+
+    scalePanelHolder = newJPanel();
+
+    idPanelHolder = newJPanel();
+
+    idSpaceFillerPanel1 = newJPanel();
+
+    annotationSpaceFillerHolder = newJPanel();
+
+    hscrollFillerPanel = newJPanel();
+
+    hscrollHolder = newJPanel();
+
+    System.out.println("GAP 3r");
+
+    try
+    {
+
+      System.out.println("GAP 3 ");
+
       jbInit();
+
+      System.out.println("GAP 4 ");
+
     } catch (Exception e)
     {
       e.printStackTrace();
     }
   }
 
+  private JScrollBar newScrollBar()
+  {
+    return new JScrollBar()
+    {
+
+      /**
+       * Overrides <code>JComponent.updateUI</code>.
+       * 
+       * @see JComponent#updateUI
+       */
+      @Override
+      public void updateUI()
+      {
+
+        System.out.println("JScrollBar.updateUI");
+        setUI(new ScrollBarUI()
+        {
+
+        });
+      }
+
+      @Override
+      public void setUI(ScrollBarUI ui)
+      {
+        System.out.println("JScrollBar.setUI");
+        // setUI(ui);
+      }
+    };
+  }
+
   private void jbInit() throws Exception
   {
 	//  annotationScroller.setBackground(Color.white);  // BH 2019
diff --git a/src/jalview/jbgui/GSplitFrame.java b/src/jalview/jbgui/GSplitFrame.java
index ed715c8..770845f 100644
--- a/src/jalview/jbgui/GSplitFrame.java
+++ b/src/jalview/jbgui/GSplitFrame.java
@@ -72,15 +72,15 @@ public class GSplitFrame extends JInternalFrame
    */
   protected void addSplitPane()
   {
-    splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT, topFrame,
-            bottomFrame);
+    splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT, topFrame.getIFrame(),
+            bottomFrame.getIFrame());
     splitPane.setVisible(true);
 
     /*
      * set divider split at 50:50, or restore saved split if loading from
      * project
      */
-    int topFrameHeight = topFrame.getHeight();
+    int topFrameHeight = topFrame.getIFrame().getHeight();
     splitPane.setDividerSize(DIVIDER_SIZE);
     if (topFrameHeight == 0)
     {
@@ -107,14 +107,17 @@ public class GSplitFrame extends JInternalFrame
     if (Platform.isAMacAndNotJS())
     {
       // this saves some space - but doesn't hide the title bar
-      topFrame.putClientProperty("JInternalFrame.isPalette", true);
+      topFrame.getIFrame().putClientProperty("JInternalFrame.isPalette", true);
       // topFrame.getRootPane().putClientProperty("Window.style", "small");
-      bottomFrame.putClientProperty("JInternalFrame.isPalette", true);
+      bottomFrame.getIFrame().putClientProperty("JInternalFrame.isPalette",
+              true);
     }
     else
     {
-	    ((BasicInternalFrameUI) topFrame.getUI()).setNorthPane(null);
-	    ((BasicInternalFrameUI) bottomFrame.getUI()).setNorthPane(null);
+      ((BasicInternalFrameUI) topFrame.getIFrame().getUI())
+              .setNorthPane(null);
+      ((BasicInternalFrameUI) bottomFrame.getIFrame().getUI())
+              .setNorthPane(null);
     }
   }
 
diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index c7b1d53..f770757 100644
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -144,23 +144,41 @@ public class CommandLineOperations
     return classpath;
   }
 
-  private Worker getJalviewDesktopRunner(boolean withAwt, String cmd,
+  private Worker getJalviewDesktopRunner(boolean headless, String cmd,
           int timeout)
   {
     // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
     // not expanded by the shell
     String classpath = getClassPath();
     String _cmd = "java "
-            + (withAwt ? "-Djava.awt.headless=true" : "")
+            + (headless ? "-Djava.awt.headless=true" : "")
             + " -classpath " + classpath + " jalview.bin.Jalview ";
     Process ls2_proc = null;
     Worker worker = null;
+
+    System.out.println("Executing " + _cmd + cmd);
     try
     {
       ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
     } catch (Throwable e1)
     {
       e1.printStackTrace();
+
+      String path = "%Java_HOME%/bin/java " + _cmd + cmd;
+
+      try
+      {
+
+        ProcessBuilder builder = new ProcessBuilder(path);
+        builder.redirectErrorStream(true);
+        ls2_proc = builder.start();
+
+      } catch (IOException e)
+      {
+        String s = e.getMessage();
+        System.out.println(s);
+      }
+
     }
     if (ls2_proc != null)
     {
@@ -183,6 +201,12 @@ public class CommandLineOperations
     return worker;
   }
 
+  private void startProcess()
+  {
+
+
+  }
+
   @BeforeTest(alwaysRun = true)
   public void initialize()
   {
@@ -212,7 +236,7 @@ public class CommandLineOperations
   @BeforeTest(alwaysRun = true)
   public void setUpForCommandLineInputOperations() throws IOException
   {
-    String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
+    String cmds = "headless -open examples/uniref50.fa -noquestionnaire -nousagestats";
     Worker worker = getJalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
     String ln = null;
     int count = 0;
diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 2f22112..75fa4a9 100644
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -1224,7 +1224,7 @@ public class SequenceTest
     assertTrue(primaryDBRefs.isEmpty());
 
     // empty dbrefs
-	sq.setDBRefs(null);
+  sq.setDBRefs(null);
     primaryDBRefs = sq.getPrimaryDBRefs();
     assertTrue(primaryDBRefs.isEmpty());
 
diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 830a759..c2fa989 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -1167,7 +1167,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     // desktop
     assertEquals(frames.length, 2,
             "PCA and the tabbed alignment view should be the only two windows on the desktop");
-    PCAPanel pcaPanel = (PCAPanel) frames[frames[0] == af ? 1 : 0];
+    PCAPanel pcaPanel = (PCAPanel) frames[frames[0] == af.getIFrame() ? 1
+            : 0];
 
     AlignmentViewPanel restoredNewView = null;
     for (AlignmentViewPanel alignpanel : Desktop.getAlignmentPanels(null))