From: James Procter <j.procter@dundee.ac.uk>
Date: Tue, 31 Jan 2023 16:17:49 +0000 (+0000)
Subject: JAL-1713 update from Jalview 2.11.3 develop
X-Git-Tag: Release_2_11_3_0~18^2~18
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3659ecfe7bb17dd25a0a6b5c94a7d9dab4525136;hp=dbdd2bd3493e0aef8aa3c0fe054c6bceedc31316;p=jalview.git

JAL-1713 update from Jalview 2.11.3 develop
Merge branch 'develop' into feature/JAL-1713_overviewInProject
regenerated jaxb classes to resolve conflicts
---

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index 1d2235e..cd05e5f 100755
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -391,6 +391,16 @@
 									</xs:complexContent>
 								</xs:complexType>
 							</xs:element>
+							<xs:element name="overview" minOccurs="0">
+							  <xs:complexType>
+								<xs:attributeGroup ref="jv:swingwindow" />
+								<xs:attribute name="showHidden" type="xs:boolean" />
+								<xs:attribute name="residueColour" type="xs:int" />
+								<xs:attribute name="gapColour" type="xs:int" />
+								<xs:attribute name="hiddenColour" type="xs:int" />
+								<xs:attribute name="title" type="xs:string" />
+							  </xs:complexType>
+							</xs:element>
 						</xs:sequence>
 						<xs:attributeGroup ref="jv:swingwindow" />
 						<xs:attribute name="conservationSelected" type="xs:boolean" />
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 0a6fabc..0b10d70 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2914,6 +2914,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       viewport.setGatherViewsHere(true);
     }
     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+
     return newap;
   }
 
@@ -3429,29 +3430,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Opens an Overview panel for the alignment, unless one is open already
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void overviewMenuItem_actionPerformed(ActionEvent e)
   {
+    boolean showHiddenRegions = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
+                false);
+    openOverviewPanel(showHiddenRegions);
+  }
+
+  public OverviewPanel openOverviewPanel(boolean showHidden)
+  {
     if (alignPanel.overviewPanel != null)
     {
-      return;
+      return alignPanel.overviewPanel;
     }
-
     JInternalFrame frame = new JInternalFrame();
-    final OverviewPanel overview = new OverviewPanel(alignPanel);
+    final OverviewPanel overview = new OverviewPanel(alignPanel, frame, showHidden);
     frame.setContentPane(overview);
-    Desktop.addInternalFrame(frame, MessageManager
-            .formatMessage("label.overview_params", new Object[]
-            { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
+    Desktop.addInternalFrame(frame, "", true, frame.getWidth(), frame.getHeight(),
             true, true);
     frame.setFrameIcon(null);
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    final AlignmentPanel thePanel = this.alignPanel; 
     frame.addInternalFrameListener(
             new javax.swing.event.InternalFrameAdapter()
             {
@@ -3460,7 +3465,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       javax.swing.event.InternalFrameEvent evt)
               {
                 overview.dispose();
-                alignPanel.setOverviewPanel(null);
+                thePanel.setOverviewPanel(null);
               }
             });
     if (getKeyListeners().length > 0)
@@ -3469,6 +3474,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     alignPanel.setOverviewPanel(overview);
+    alignPanel.setOverviewTitle(this);
+    
+    return overview;
   }
 
   @Override
@@ -4960,7 +4968,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     if (index > -1)
     {
+      /*
+       * update current Overview window title (if there is one)
+       * to add view name "Original" if necessary
+       */
+      alignPanel.setOverviewTitle(this);
+      
+      /*
+       * switch panels and set Overview title (if there is one
+       * because it was opened automatically)
+       */
       alignPanel = alignPanels.get(index);
+      alignPanel.setOverviewTitle(this);
+
       viewport = alignPanel.av;
       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
       setMenusFromViewport(viewport);
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index e84aae0..e545776 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1742,4 +1742,42 @@ public class AlignmentPanel extends GAlignmentPanel implements
     return calculationDialog;
   }
 
+  /**
+   * Constructs and sets the title for the Overview window (if there is one),
+   * including the align frame's title, and view name (if applicable). Returns
+   * the title, or null if this panel has no Overview window open.
+   * 
+   * @param alignFrame
+   * @return
+   */
+  public String setOverviewTitle(AlignFrame alignFrame)
+  {
+    if (this.overviewPanel == null)
+    {
+      return null;
+    }
+    String overviewTitle = MessageManager
+            .formatMessage("label.overview_params", new Object[]
+            { alignFrame.getTitle() });
+    String viewName = getViewName();
+    if (viewName != null)
+    {
+      overviewTitle += (" " + viewName);
+    }
+    overviewPanel.setTitle(overviewTitle);
+    return overviewTitle;
+  }
+
+  /**
+   * If this alignment panel has an Overview panel open, closes it
+   */
+  public void closeOverviewPanel()
+  {
+    if (overviewPanel != null)
+    {
+      overviewPanel.close();
+      overviewPanel = null;
+    }
+  }
+
 }
diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java
index 470fd64..586ac2c 100644
--- a/src/jalview/gui/OverviewCanvas.java
+++ b/src/jalview/gui/OverviewCanvas.java
@@ -20,13 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.api.AlignViewportI;
-import jalview.bin.Cache;
-import jalview.renderer.OverviewRenderer;
-import jalview.renderer.OverviewResColourFinder;
-import jalview.viewmodel.OverviewDimensions;
-import jalview.viewmodel.seqfeatures.FeatureRendererModel;
-
 import java.awt.Color;
 import java.awt.Dimension;
 import java.awt.Graphics;
@@ -34,8 +27,26 @@ import java.awt.image.BufferedImage;
 
 import javax.swing.JPanel;
 
+import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
+import jalview.renderer.OverviewRenderer;
+import jalview.renderer.OverviewResColourFinder;
+import jalview.viewmodel.OverviewDimensions;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
+
 public class OverviewCanvas extends JPanel
 {
+  public static final Color OVERVIEW_DEFAULT_GAP = Color.lightGray;
+
+  public static final Color OVERVIEW_DEFAULT_LEGACY_GAP = Color.white;
+
+  public static final Color OVERVIEW_DEFAULT_RESIDUE = Color.white;
+
+  public static final Color OVERVIEW_DEFAULT_LEGACY_RESIDUE = Color.lightGray;
+
+  public static final Color OVERVIEW_DEFAULT_HIDDEN = Color.darkGray
+          .darker();
+
   private static final Color TRANS_GREY = new Color(100, 100, 100, 25);
 
   // This is set true if the alignment view changes whilst
@@ -79,10 +90,12 @@ public class OverviewCanvas extends JPanel
 
     boolean useLegacy = Cache.getDefault(Preferences.USE_LEGACY_GAP, false);
     Color gapCol = Cache.getDefaultColour(Preferences.GAP_COLOUR,
-            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
+            OVERVIEW_DEFAULT_GAP);
     Color hiddenCol = Cache.getDefaultColour(Preferences.HIDDEN_COLOUR,
-            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
-    cf = new OverviewResColourFinder(useLegacy, gapCol, hiddenCol);
+            OVERVIEW_DEFAULT_HIDDEN);
+    Color residueCol = useLegacy ? OVERVIEW_DEFAULT_LEGACY_RESIDUE : OVERVIEW_DEFAULT_RESIDUE;
+    
+    cf = new OverviewResColourFinder(gapCol, residueCol, hiddenCol);
 
     setSize(od.getWidth(), od.getHeight());
   }
@@ -268,4 +281,31 @@ public class OverviewCanvas extends JPanel
       }
     }
   }
+
+  public Color getGapColour()
+  {
+    return cf.getGapColour();
+  }
+
+  public Color getHiddenColour()
+  {
+    return cf.getHiddenColour();
+  }
+
+  public Color getResidueColour()
+  {
+    return cf.getResidueColour();
+  }
+
+  /**
+   * Sets the colours to use for gaps, residues and hidden regions
+   * 
+   * @param gaps
+   * @param residues
+   * @param hidden
+   */
+  public void setColours(Color gaps, Color residues, Color hidden)
+  {
+    cf = new OverviewResColourFinder(gaps, residues, hidden);
+  }
 }
diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index adde919..872d142 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -20,18 +20,10 @@
  */
 package jalview.gui;
 
-import jalview.bin.Cache;
-import jalview.renderer.OverviewRenderer;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.viewmodel.OverviewDimensions;
-import jalview.viewmodel.OverviewDimensionsHideHidden;
-import jalview.viewmodel.OverviewDimensionsShowHidden;
-import jalview.viewmodel.ViewportListenerI;
-
 import java.awt.BorderLayout;
 import java.awt.Cursor;
 import java.awt.Dimension;
+import java.awt.Rectangle;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.ComponentAdapter;
@@ -48,6 +40,14 @@ import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
 import javax.swing.SwingUtilities;
 
+import jalview.renderer.OverviewRenderer;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.OverviewDimensions;
+import jalview.viewmodel.OverviewDimensionsHideHidden;
+import jalview.viewmodel.OverviewDimensionsShowHidden;
+import jalview.viewmodel.ViewportListenerI;
+
 /**
  * Panel displaying an overview of the full alignment, with an interactive box
  * representing the viewport onto the alignment.
@@ -67,6 +67,8 @@ public class OverviewPanel extends JPanel
 
   private AlignmentPanel ap;
 
+  private JInternalFrame internalFrame;
+
   protected JCheckBoxMenuItem displayToggle;
 
   protected boolean showHidden = true;
@@ -80,14 +82,18 @@ public class OverviewPanel extends JPanel
    * 
    * @param alPanel
    *          The alignment panel which is shown in the overview panel
+   * @param frame
+   * @param isShowHidden
+   *          TODO
    */
-  public OverviewPanel(AlignmentPanel alPanel)
+  public OverviewPanel(AlignmentPanel alPanel, JInternalFrame frame,
+          boolean isShowHidden)
   {
     this.av = alPanel.av;
     this.ap = alPanel;
+    this.internalFrame = frame;
 
-    showHidden = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
-            false);
+    showHidden = isShowHidden;
     if (showHidden)
     {
       od = new OverviewDimensionsShowHidden(av.getRanges(),
@@ -420,6 +426,68 @@ public class OverviewPanel extends JPanel
       oviewCanvas = null;
       ap = null;
       od = null;
+      internalFrame = null;
     }
   }
+
+  public boolean isShowHiddenRegions()
+  {
+    return showHidden;
+  }
+
+  public OverviewCanvas getCanvas()
+  {
+    return oviewCanvas;
+  }
+
+  /**
+   * Sets the title of the enclosing frame
+   * 
+   * @param title
+   */
+  public void setTitle(String title)
+  {
+    internalFrame.setTitle(title);
+  }
+
+  /**
+   * Returns the title of the enclosing frame
+   * 
+   * @return title
+   */
+  public String getTitle()
+  {
+    return internalFrame.getTitle();
+  }
+
+  /**
+   * Sets the bounds of the frame holding the Overview panel
+   * 
+   * @param xpos
+   * @param ypos
+   * @param width
+   * @param height
+   */
+  public void setFrameBounds(int xpos, int ypos, int width, int height)
+  {
+    internalFrame.setBounds(xpos, ypos, width, height);
+  }
+
+  /**
+   * Returns the bounds of the enclosing frame
+   * 
+   * @return
+   */
+  public Rectangle getFrameBounds()
+  {
+    return internalFrame.getBounds();
+  }
+
+  /**
+   * Closes the frame containing the overview panel
+   */
+  public void close()
+  {
+    internalFrame.dispose();
+  }
 }
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 2f0257f..493deee 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -386,9 +386,9 @@ public class Preferences extends GPreferences
      * Set overview panel defaults
      */
     gapColour.setBackground(Cache.getDefaultColour(GAP_COLOUR,
-            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
+            OverviewCanvas.OVERVIEW_DEFAULT_GAP));
     hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR,
-            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
+            OverviewCanvas.OVERVIEW_DEFAULT_HIDDEN));
     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
     gapLabel.setEnabled(!useLegacyGap.isSelected());
     gapColour.setEnabled(!useLegacyGap.isSelected());
@@ -1307,13 +1307,11 @@ public class Preferences extends GPreferences
     boolean enabled = useLegacyGap.isSelected();
     if (enabled)
     {
-      gapColour.setBackground(
-              jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
+      gapColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_LEGACY_GAP);
     }
     else
     {
-      gapColour.setBackground(
-              jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
+      gapColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_GAP);
     }
     gapColour.setEnabled(!enabled);
     gapLabel.setEnabled(!enabled);
@@ -1325,8 +1323,7 @@ public class Preferences extends GPreferences
     useLegacyGap.setSelected(false);
     useLegacyGaps_actionPerformed(null);
     showHiddenAtStart.setSelected(false);
-    hiddenColour.setBackground(
-            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
+    hiddenColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_HIDDEN);
   }
 
   @Override
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index ffeb53d..a4d4043 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -485,6 +485,12 @@ public class FileLoader implements Runnable
               // that perform queries to find the 'current working alignment'
               Desktop.addInternalFrame(alignFrame, title,
                       AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+
+              /*
+               * for an Overview automatically opened with alignment,
+               * set its title now alignFrame title has been set
+               */
+              alignFrame.alignPanel.setOverviewTitle(alignFrame);
             }
 
             try
diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index c8f9be6..4b9c348 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -112,6 +112,7 @@ import jalview.gui.AppVarna;
 import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
 import jalview.gui.OOMWarning;
+import jalview.gui.OverviewPanel;
 import jalview.gui.PCAPanel;
 import jalview.gui.PaintRefresher;
 import jalview.gui.SplitFrame;
@@ -185,6 +186,7 @@ import jalview.xml.binding.jalview.JalviewModel.UserColours;
 import jalview.xml.binding.jalview.JalviewModel.Viewport;
 import jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam;
 import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns;
+import jalview.xml.binding.jalview.JalviewModel.Viewport.Overview;
 import jalview.xml.binding.jalview.JalviewUserColours;
 import jalview.xml.binding.jalview.JalviewUserColours.Colour;
 import jalview.xml.binding.jalview.MapListType.MapListFrom;
@@ -1492,6 +1494,23 @@ public class Jalview2XML
       view.setStartRes(vpRanges.getStartRes());
       view.setStartSeq(vpRanges.getStartSeq());
 
+      OverviewPanel ov = ap.getOverviewPanel();
+      if (ov != null)
+      {
+        Overview overview = new Overview();
+        overview.setTitle(ov.getTitle());
+        Rectangle bounds = ov.getFrameBounds();
+        overview.setXpos(bounds.x);
+        overview.setYpos(bounds.y);
+        overview.setWidth(bounds.width);
+        overview.setHeight(bounds.height);
+        overview.setShowHidden(ov.isShowHiddenRegions());
+        overview.setGapColour(ov.getCanvas().getGapColour().getRGB());
+        overview.setResidueColour(
+                ov.getCanvas().getResidueColour().getRGB());
+        overview.setHiddenColour(ov.getCanvas().getHiddenColour().getRGB());
+        view.setOverview(overview);
+      }
       if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
       {
         view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
@@ -4093,7 +4112,7 @@ public class Jalview2XML
     }
 
     /*
-     * Load any trees, PDB structures and viewers
+     * Load any trees, PDB structures and viewers, Overview
      * 
      * Not done if flag is false (when this method is used for New View)
      */
@@ -4103,12 +4122,44 @@ public class Jalview2XML
       loadPCAViewers(jalviewModel, ap);
       loadPDBStructures(jprovider, jseqs, af, ap);
       loadRnaViewers(jprovider, jseqs, ap);
+      loadOverview(view, af);
     }
     // and finally return.
     return af;
   }
 
   /**
+   * Load Overview window, restoring colours, 'show hidden regions' flag, title
+   * and geometry as saved
+   * 
+   * @param view
+   * @param af
+   */
+  protected void loadOverview(Viewport view, AlignFrame af)
+  {
+    /*
+     * first close any Overview that was opened automatically
+     * (if so configured in Preferences) so that the view is
+     * restored in the same state as saved
+     */
+    af.alignPanel.closeOverviewPanel();
+
+    Overview overview = view.getOverview();
+    if (overview != null)
+    {
+      OverviewPanel overviewPanel = af
+              .openOverviewPanel(overview.isShowHidden());
+      overviewPanel.setTitle(overview.getTitle());
+      overviewPanel.setFrameBounds(overview.getXpos(), overview.getYpos(),
+              overview.getWidth(), overview.getHeight());
+      Color gap = new Color(overview.getGapColour());
+      Color residue = new Color(overview.getResidueColour());
+      Color hidden = new Color(overview.getHiddenColour());
+      overviewPanel.getCanvas().setColours(gap, residue, hidden);
+    }
+  }
+
+  /**
    * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
    * panel is restored from separate jar entries, two (gapped and trimmed) per
    * sequence and secondary structure.
@@ -5031,6 +5082,7 @@ public class Jalview2XML
     {
       splitFrameCandidates.put(view, af);
     }
+
     return af;
   }
 
diff --git a/src/jalview/renderer/OverviewRenderer.java b/src/jalview/renderer/OverviewRenderer.java
index 1b5d5da..1ff032b 100644
--- a/src/jalview/renderer/OverviewRenderer.java
+++ b/src/jalview/renderer/OverviewRenderer.java
@@ -225,7 +225,7 @@ public class OverviewRenderer
   int getColumnColourFromSequence(SequenceGroup[] allGroups, SequenceI seq,
           int lastcol)
   {
-    Color color = resColFinder.GAP_COLOUR;
+    Color color = resColFinder.gapColour;
 
     if ((seq != null) && (seq.getLength() > lastcol))
     {
diff --git a/src/jalview/renderer/OverviewResColourFinder.java b/src/jalview/renderer/OverviewResColourFinder.java
index 57cae1c..ef4d04b 100644
--- a/src/jalview/renderer/OverviewResColourFinder.java
+++ b/src/jalview/renderer/OverviewResColourFinder.java
@@ -20,68 +20,60 @@
  */
 package jalview.renderer;
 
+import java.awt.Color;
+
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
 
-import java.awt.Color;
-
 public class OverviewResColourFinder extends ResidueColourFinder
 {
-  final Color GAP_COLOUR; // default colour to use at gaps
-
-  final Color RESIDUE_COLOUR; // default colour to use at residues
-
-  final Color HIDDEN_COLOUR; // colour for hidden regions
-
-  boolean useLegacy = false;
-
-  public static final Color OVERVIEW_DEFAULT_GAP = Color.lightGray;
+  /*
+   * colour for gaps (unless overridden by colour scheme)
+   * - as set in Preferences, _or_ read from a project file
+   */
+  Color gapColour;
 
-  public static final Color OVERVIEW_DEFAULT_LEGACY_GAP = Color.white;
+  /*
+   * colour for residues if no colour scheme set (before feature colouring)
+   * - as set in Preferences, _or_ read from a project file
+   */
+  Color residueColour;
 
-  public static final Color OVERVIEW_DEFAULT_HIDDEN = Color.darkGray
-          .darker();
+  /*
+   * colour for hidden regions
+   * - as set in Preferences, _or_ read from a project file
+   */
+  Color hiddenColour;
 
   /**
    * Constructor without colour settings (used by applet)
+   * @deprecated
    */
+  @Deprecated
   public OverviewResColourFinder()
   {
-    this(false, OVERVIEW_DEFAULT_GAP, OVERVIEW_DEFAULT_HIDDEN);
+    this(Color.lightGray, Color.white, Color.darkGray.darker());
   }
 
   /**
-   * Constructor with colour settings
+   * Constructor given default colours for gaps, residues and hidden regions
    * 
-   * @param useLegacyColouring
-   *          whether to use legacy gap colouring (white gaps, grey residues)
-   * @param gapCol
-   *          gap colour if not legacy
-   * @param hiddenCol
-   *          hidden region colour (transparency applied by rendering code)
+   * @param gaps
+   * @param residues
+   * @param hidden
    */
-  public OverviewResColourFinder(boolean useLegacyColouring, Color gapCol,
-          Color hiddenCol)
+  public OverviewResColourFinder(Color gaps, Color residues, Color hidden)
   {
-    if (useLegacyColouring)
-    {
-      GAP_COLOUR = Color.white;
-      RESIDUE_COLOUR = Color.lightGray;
-      HIDDEN_COLOUR = hiddenCol;
-    }
-    else
-    {
-      GAP_COLOUR = gapCol;
-      RESIDUE_COLOUR = Color.white;
-      HIDDEN_COLOUR = hiddenCol;
-    }
+    gapColour = gaps;
+    residueColour = residues;
+    hiddenColour = hidden;
   }
 
   @Override
   public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
   {
-    Color resBoxColour = RESIDUE_COLOUR;
+    Color resBoxColour = residueColour;
     char currentChar = seq.getCharAt(i);
 
     // In the overview window, gaps are coloured grey, unless the colour scheme
@@ -92,7 +84,7 @@ public class OverviewResColourFinder extends ResidueColourFinder
       if (Comparison.isGap(currentChar)
               && (!shader.getColourScheme().hasGapColour()))
       {
-        resBoxColour = GAP_COLOUR;
+        resBoxColour = gapColour;
       }
       else
       {
@@ -101,7 +93,7 @@ public class OverviewResColourFinder extends ResidueColourFinder
     }
     else if (Comparison.isGap(currentChar))
     {
-      resBoxColour = GAP_COLOUR;
+      resBoxColour = gapColour;
     }
 
     return resBoxColour;
@@ -132,12 +124,34 @@ public class OverviewResColourFinder extends ResidueColourFinder
   }
 
   /**
-   * Supply hidden colour
+   * Returns the colour used for hidden regions
+   * 
+   * @return
+   */
+  public Color getHiddenColour()
+  {
+    return hiddenColour;
+  }
+
+  /**
+   * Returns the colour used for gaps, if not overridden by the alignment colour
+   * scheme
+   * 
+   * @return
+   */
+  public Color getGapColour()
+  {
+    return gapColour;
+  }
+
+  /**
+   * Returns the colour used for residues (before applying any feature
+   * colouring) if there is no alignment colour scheme
    * 
-   * @return colour of hidden regions
+   * @return
    */
-  protected Color getHiddenColour()
+  public Color getResidueColour()
   {
-    return HIDDEN_COLOUR;
+    return residueColour;
   }
 }
diff --git a/src/jalview/xml/binding/embl/EntrySetType.java b/src/jalview/xml/binding/embl/EntrySetType.java
index 6e73e7b..7c061d7 100644
--- a/src/jalview/xml/binding/embl/EntrySetType.java
+++ b/src/jalview/xml/binding/embl/EntrySetType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2018.09.14 at 02:46:00 PM BST 
+// Generated on: 2023.01.31 at 04:07:09 PM GMT 
 //
 
+
 package jalview.xml.binding.embl;
 
 import java.util.ArrayList;
@@ -14,13 +15,11 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>
- * Java class for EntrySetType complex type.
+ * <p>Java class for EntrySetType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="EntrySetType">
@@ -37,42 +36,41 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "EntrySetType", propOrder = { "entry" })
-public class EntrySetType
-{
+@XmlType(name = "EntrySetType", propOrder = {
+    "entry"
+})
+public class EntrySetType {
 
-  @XmlElement(required = true)
-  protected List<EntryType> entry;
+    @XmlElement(required = true)
+    protected List<EntryType> entry;
 
-  /**
-   * Gets the value of the entry property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the entry property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getEntry().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link EntryType }
-   * 
-   * 
-   */
-  public List<EntryType> getEntry()
-  {
-    if (entry == null)
-    {
-      entry = new ArrayList<EntryType>();
+    /**
+     * Gets the value of the entry property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the entry property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getEntry().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link EntryType }
+     * 
+     * 
+     */
+    public List<EntryType> getEntry() {
+        if (entry == null) {
+            entry = new ArrayList<EntryType>();
+        }
+        return this.entry;
     }
-    return this.entry;
-  }
 
 }
diff --git a/src/jalview/xml/binding/embl/EntryType.java b/src/jalview/xml/binding/embl/EntryType.java
index 6bdc35f..2791f66 100644
--- a/src/jalview/xml/binding/embl/EntryType.java
+++ b/src/jalview/xml/binding/embl/EntryType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2018.09.14 at 02:46:00 PM BST 
+// Generated on: 2023.01.31 at 04:07:09 PM GMT 
 //
 
+
 package jalview.xml.binding.embl;
 
 import java.math.BigInteger;
@@ -19,13 +20,11 @@ import javax.xml.bind.annotation.XmlSchemaType;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.datatype.XMLGregorianCalendar;
 
+
 /**
- * <p>
- * Java class for EntryType complex type.
+ * <p>Java class for EntryType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="EntryType">
@@ -226,1666 +225,669 @@ import javax.xml.datatype.XMLGregorianCalendar;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "EntryType",
-  propOrder =
-  { "secondaryAccession", "projectAccession", "description", "comment",
-      "keyword", "reference", "xref", "feature", "assembly", "contig",
-      "sequence" })
-public class EntryType
-{
-
-  protected List<String> secondaryAccession;
-
-  protected List<String> projectAccession;
-
-  @XmlElement(required = true)
-  protected String description;
-
-  protected String comment;
-
-  protected List<String> keyword;
-
-  protected List<EntryType.Reference> reference;
-
-  protected List<XrefType> xref;
-
-  protected List<EntryType.Feature> feature;
-
-  protected EntryType.Assembly assembly;
-
-  protected EntryType.Contig contig;
-
-  protected String sequence;
-
-  @XmlAttribute(name = "accession", required = true)
-  protected String accession;
-
-  @XmlAttribute(name = "version", required = true)
-  protected BigInteger version;
-
-  @XmlAttribute(name = "entryVersion")
-  protected BigInteger entryVersion;
-
-  @XmlAttribute(name = "dataClass", required = true)
-  protected String dataClass;
-
-  @XmlAttribute(name = "taxonomicDivision", required = true)
-  protected String taxonomicDivision;
-
-  @XmlAttribute(name = "moleculeType", required = true)
-  protected String moleculeType;
-
-  @XmlAttribute(name = "sequenceLength", required = true)
-  protected BigInteger sequenceLength;
-
-  @XmlAttribute(name = "topology", required = true)
-  protected String topology;
-
-  @XmlAttribute(name = "firstPublic")
-  @XmlSchemaType(name = "date")
-  protected XMLGregorianCalendar firstPublic;
-
-  @XmlAttribute(name = "firstPublicRelease")
-  protected BigInteger firstPublicRelease;
-
-  @XmlAttribute(name = "lastUpdated")
-  @XmlSchemaType(name = "date")
-  protected XMLGregorianCalendar lastUpdated;
-
-  @XmlAttribute(name = "lastUpdatedRelease")
-  protected BigInteger lastUpdatedRelease;
-
-  /**
-   * Gets the value of the secondaryAccession property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the secondaryAccession property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getSecondaryAccession().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link String }
-   * 
-   * 
-   */
-  public List<String> getSecondaryAccession()
-  {
-    if (secondaryAccession == null)
-    {
-      secondaryAccession = new ArrayList<String>();
-    }
-    return this.secondaryAccession;
-  }
-
-  /**
-   * Gets the value of the projectAccession property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the projectAccession property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getProjectAccession().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link String }
-   * 
-   * 
-   */
-  public List<String> getProjectAccession()
-  {
-    if (projectAccession == null)
-    {
-      projectAccession = new ArrayList<String>();
-    }
-    return this.projectAccession;
-  }
-
-  /**
-   * Gets the value of the description property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDescription()
-  {
-    return description;
-  }
-
-  /**
-   * Sets the value of the description property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDescription(String value)
-  {
-    this.description = value;
-  }
-
-  /**
-   * Gets the value of the comment property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getComment()
-  {
-    return comment;
-  }
-
-  /**
-   * Sets the value of the comment property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setComment(String value)
-  {
-    this.comment = value;
-  }
-
-  /**
-   * Gets the value of the keyword property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the keyword property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getKeyword().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link String }
-   * 
-   * 
-   */
-  public List<String> getKeyword()
-  {
-    if (keyword == null)
-    {
-      keyword = new ArrayList<String>();
-    }
-    return this.keyword;
-  }
-
-  /**
-   * Gets the value of the reference property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the reference property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getReference().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link EntryType.Reference }
-   * 
-   * 
-   */
-  public List<EntryType.Reference> getReference()
-  {
-    if (reference == null)
-    {
-      reference = new ArrayList<EntryType.Reference>();
-    }
-    return this.reference;
-  }
-
-  /**
-   * Gets the value of the xref property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the xref property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getXref().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link XrefType }
-   * 
-   * 
-   */
-  public List<XrefType> getXref()
-  {
-    if (xref == null)
-    {
-      xref = new ArrayList<XrefType>();
-    }
-    return this.xref;
-  }
-
-  /**
-   * Gets the value of the feature property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the feature property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getFeature().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link EntryType.Feature }
-   * 
-   * 
-   */
-  public List<EntryType.Feature> getFeature()
-  {
-    if (feature == null)
-    {
-      feature = new ArrayList<EntryType.Feature>();
-    }
-    return this.feature;
-  }
-
-  /**
-   * Gets the value of the assembly property.
-   * 
-   * @return possible object is {@link EntryType.Assembly }
-   * 
-   */
-  public EntryType.Assembly getAssembly()
-  {
-    return assembly;
-  }
-
-  /**
-   * Sets the value of the assembly property.
-   * 
-   * @param value
-   *          allowed object is {@link EntryType.Assembly }
-   * 
-   */
-  public void setAssembly(EntryType.Assembly value)
-  {
-    this.assembly = value;
-  }
-
-  /**
-   * Gets the value of the contig property.
-   * 
-   * @return possible object is {@link EntryType.Contig }
-   * 
-   */
-  public EntryType.Contig getContig()
-  {
-    return contig;
-  }
-
-  /**
-   * Sets the value of the contig property.
-   * 
-   * @param value
-   *          allowed object is {@link EntryType.Contig }
-   * 
-   */
-  public void setContig(EntryType.Contig value)
-  {
-    this.contig = value;
-  }
-
-  /**
-   * Gets the value of the sequence property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getSequence()
-  {
-    return sequence;
-  }
-
-  /**
-   * Sets the value of the sequence property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setSequence(String value)
-  {
-    this.sequence = value;
-  }
-
-  /**
-   * Gets the value of the accession property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getAccession()
-  {
-    return accession;
-  }
-
-  /**
-   * Sets the value of the accession property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setAccession(String value)
-  {
-    this.accession = value;
-  }
-
-  /**
-   * Gets the value of the version property.
-   * 
-   * @return possible object is {@link BigInteger }
-   * 
-   */
-  public BigInteger getVersion()
-  {
-    return version;
-  }
-
-  /**
-   * Sets the value of the version property.
-   * 
-   * @param value
-   *          allowed object is {@link BigInteger }
-   * 
-   */
-  public void setVersion(BigInteger value)
-  {
-    this.version = value;
-  }
-
-  /**
-   * Gets the value of the entryVersion property.
-   * 
-   * @return possible object is {@link BigInteger }
-   * 
-   */
-  public BigInteger getEntryVersion()
-  {
-    return entryVersion;
-  }
-
-  /**
-   * Sets the value of the entryVersion property.
-   * 
-   * @param value
-   *          allowed object is {@link BigInteger }
-   * 
-   */
-  public void setEntryVersion(BigInteger value)
-  {
-    this.entryVersion = value;
-  }
-
-  /**
-   * Gets the value of the dataClass property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDataClass()
-  {
-    return dataClass;
-  }
-
-  /**
-   * Sets the value of the dataClass property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDataClass(String value)
-  {
-    this.dataClass = value;
-  }
-
-  /**
-   * Gets the value of the taxonomicDivision property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getTaxonomicDivision()
-  {
-    return taxonomicDivision;
-  }
-
-  /**
-   * Sets the value of the taxonomicDivision property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setTaxonomicDivision(String value)
-  {
-    this.taxonomicDivision = value;
-  }
-
-  /**
-   * Gets the value of the moleculeType property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getMoleculeType()
-  {
-    return moleculeType;
-  }
-
-  /**
-   * Sets the value of the moleculeType property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setMoleculeType(String value)
-  {
-    this.moleculeType = value;
-  }
-
-  /**
-   * Gets the value of the sequenceLength property.
-   * 
-   * @return possible object is {@link BigInteger }
-   * 
-   */
-  public BigInteger getSequenceLength()
-  {
-    return sequenceLength;
-  }
-
-  /**
-   * Sets the value of the sequenceLength property.
-   * 
-   * @param value
-   *          allowed object is {@link BigInteger }
-   * 
-   */
-  public void setSequenceLength(BigInteger value)
-  {
-    this.sequenceLength = value;
-  }
-
-  /**
-   * Gets the value of the topology property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getTopology()
-  {
-    return topology;
-  }
-
-  /**
-   * Sets the value of the topology property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setTopology(String value)
-  {
-    this.topology = value;
-  }
-
-  /**
-   * Gets the value of the firstPublic property.
-   * 
-   * @return possible object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public XMLGregorianCalendar getFirstPublic()
-  {
-    return firstPublic;
-  }
-
-  /**
-   * Sets the value of the firstPublic property.
-   * 
-   * @param value
-   *          allowed object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public void setFirstPublic(XMLGregorianCalendar value)
-  {
-    this.firstPublic = value;
-  }
-
-  /**
-   * Gets the value of the firstPublicRelease property.
-   * 
-   * @return possible object is {@link BigInteger }
-   * 
-   */
-  public BigInteger getFirstPublicRelease()
-  {
-    return firstPublicRelease;
-  }
-
-  /**
-   * Sets the value of the firstPublicRelease property.
-   * 
-   * @param value
-   *          allowed object is {@link BigInteger }
-   * 
-   */
-  public void setFirstPublicRelease(BigInteger value)
-  {
-    this.firstPublicRelease = value;
-  }
-
-  /**
-   * Gets the value of the lastUpdated property.
-   * 
-   * @return possible object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public XMLGregorianCalendar getLastUpdated()
-  {
-    return lastUpdated;
-  }
-
-  /**
-   * Sets the value of the lastUpdated property.
-   * 
-   * @param value
-   *          allowed object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public void setLastUpdated(XMLGregorianCalendar value)
-  {
-    this.lastUpdated = value;
-  }
-
-  /**
-   * Gets the value of the lastUpdatedRelease property.
-   * 
-   * @return possible object is {@link BigInteger }
-   * 
-   */
-  public BigInteger getLastUpdatedRelease()
-  {
-    return lastUpdatedRelease;
-  }
-
-  /**
-   * Sets the value of the lastUpdatedRelease property.
-   * 
-   * @param value
-   *          allowed object is {@link BigInteger }
-   * 
-   */
-  public void setLastUpdatedRelease(BigInteger value)
-  {
-    this.lastUpdatedRelease = value;
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;sequence>
-   *         &lt;element name="range" maxOccurs="unbounded">
-   *           &lt;complexType>
-   *             &lt;complexContent>
-   *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                 &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                 &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                 &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                 &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                 &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *               &lt;/restriction>
-   *             &lt;/complexContent>
-   *           &lt;/complexType>
-   *         &lt;/element>
-   *       &lt;/sequence>
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "range" })
-  public static class Assembly
-  {
-
+@XmlType(name = "EntryType", propOrder = {
+    "secondaryAccession",
+    "projectAccession",
+    "description",
+    "comment",
+    "keyword",
+    "reference",
+    "xref",
+    "feature",
+    "assembly",
+    "contig",
+    "sequence"
+})
+public class EntryType {
+
+    protected List<String> secondaryAccession;
+    protected List<String> projectAccession;
     @XmlElement(required = true)
-    protected List<EntryType.Assembly.Range> range;
+    protected String description;
+    protected String comment;
+    protected List<String> keyword;
+    protected List<EntryType.Reference> reference;
+    protected List<XrefType> xref;
+    protected List<EntryType.Feature> feature;
+    protected EntryType.Assembly assembly;
+    protected EntryType.Contig contig;
+    protected String sequence;
+    @XmlAttribute(name = "accession", required = true)
+    protected String accession;
+    @XmlAttribute(name = "version", required = true)
+    protected BigInteger version;
+    @XmlAttribute(name = "entryVersion")
+    protected BigInteger entryVersion;
+    @XmlAttribute(name = "dataClass", required = true)
+    protected String dataClass;
+    @XmlAttribute(name = "taxonomicDivision", required = true)
+    protected String taxonomicDivision;
+    @XmlAttribute(name = "moleculeType", required = true)
+    protected String moleculeType;
+    @XmlAttribute(name = "sequenceLength", required = true)
+    protected BigInteger sequenceLength;
+    @XmlAttribute(name = "topology", required = true)
+    protected String topology;
+    @XmlAttribute(name = "firstPublic")
+    @XmlSchemaType(name = "date")
+    protected XMLGregorianCalendar firstPublic;
+    @XmlAttribute(name = "firstPublicRelease")
+    protected BigInteger firstPublicRelease;
+    @XmlAttribute(name = "lastUpdated")
+    @XmlSchemaType(name = "date")
+    protected XMLGregorianCalendar lastUpdated;
+    @XmlAttribute(name = "lastUpdatedRelease")
+    protected BigInteger lastUpdatedRelease;
 
     /**
-     * Gets the value of the range property.
+     * Gets the value of the secondaryAccession property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the range property.
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the secondaryAccession property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
-     * 
      * <pre>
-     * getRange().add(newItem);
+     *    getSecondaryAccession().add(newItem);
      * </pre>
      * 
      * 
      * <p>
      * Objects of the following type(s) are allowed in the list
-     * {@link EntryType.Assembly.Range }
+     * {@link String }
      * 
      * 
      */
-    public List<EntryType.Assembly.Range> getRange()
-    {
-      if (range == null)
-      {
-        range = new ArrayList<EntryType.Assembly.Range>();
-      }
-      return this.range;
+    public List<String> getSecondaryAccession() {
+        if (secondaryAccession == null) {
+            secondaryAccession = new ArrayList<String>();
+        }
+        return this.secondaryAccession;
     }
 
     /**
-     * <p>
-     * Java class for anonymous complex type.
+     * Gets the value of the projectAccession property.
      * 
      * <p>
-     * The following schema fragment specifies the expected content contained
-     * within this class.
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the projectAccession property.
      * 
+     * <p>
+     * For example, to add a new item, do as follows:
      * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
+     *    getProjectAccession().add(newItem);
      * </pre>
      * 
      * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
+     * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class Range
-    {
-
-      @XmlAttribute(name = "begin", required = true)
-      protected BigInteger begin;
-
-      @XmlAttribute(name = "end", required = true)
-      protected BigInteger end;
-
-      @XmlAttribute(name = "primaryBegin")
-      protected BigInteger primaryBegin;
-
-      @XmlAttribute(name = "primaryEnd")
-      protected BigInteger primaryEnd;
-
-      @XmlAttribute(name = "accession", required = true)
-      protected String accession;
-
-      @XmlAttribute(name = "version", required = true)
-      protected BigInteger version;
-
-      @XmlAttribute(name = "complement")
-      protected Boolean complement;
-
-      /**
-       * Gets the value of the begin property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getBegin()
-      {
-        return begin;
-      }
-
-      /**
-       * Sets the value of the begin property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setBegin(BigInteger value)
-      {
-        this.begin = value;
-      }
-
-      /**
-       * Gets the value of the end property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getEnd()
-      {
-        return end;
-      }
-
-      /**
-       * Sets the value of the end property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setEnd(BigInteger value)
-      {
-        this.end = value;
-      }
-
-      /**
-       * Gets the value of the primaryBegin property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getPrimaryBegin()
-      {
-        return primaryBegin;
-      }
-
-      /**
-       * Sets the value of the primaryBegin property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setPrimaryBegin(BigInteger value)
-      {
-        this.primaryBegin = value;
-      }
-
-      /**
-       * Gets the value of the primaryEnd property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getPrimaryEnd()
-      {
-        return primaryEnd;
-      }
-
-      /**
-       * Sets the value of the primaryEnd property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setPrimaryEnd(BigInteger value)
-      {
-        this.primaryEnd = value;
-      }
-
-      /**
-       * Gets the value of the accession property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getAccession()
-      {
-        return accession;
-      }
-
-      /**
-       * Sets the value of the accession property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setAccession(String value)
-      {
-        this.accession = value;
-      }
-
-      /**
-       * Gets the value of the version property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getVersion()
-      {
-        return version;
-      }
-
-      /**
-       * Sets the value of the version property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setVersion(BigInteger value)
-      {
-        this.version = value;
-      }
-
-      /**
-       * Gets the value of the complement property.
-       * 
-       * @return possible object is {@link Boolean }
-       * 
-       */
-      public boolean isComplement()
-      {
-        if (complement == null)
-        {
-          return false;
-        }
-        else
-        {
-          return complement;
+    public List<String> getProjectAccession() {
+        if (projectAccession == null) {
+            projectAccession = new ArrayList<String>();
         }
-      }
-
-      /**
-       * Sets the value of the complement property.
-       * 
-       * @param value
-       *          allowed object is {@link Boolean }
-       * 
-       */
-      public void setComplement(Boolean value)
-      {
-        this.complement = value;
-      }
+        return this.projectAccession;
+    }
+
+    /**
+     * Gets the value of the description property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDescription() {
+        return description;
+    }
 
+    /**
+     * Sets the value of the description property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDescription(String value) {
+        this.description = value;
+    }
+
+    /**
+     * Gets the value of the comment property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getComment() {
+        return comment;
     }
 
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;sequence>
-   *         &lt;choice maxOccurs="unbounded" minOccurs="0">
-   *           &lt;element name="range">
-   *             &lt;complexType>
-   *               &lt;complexContent>
-   *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                   &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                   &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                   &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                   &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                   &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                   &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                   &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *                 &lt;/restriction>
-   *               &lt;/complexContent>
-   *             &lt;/complexType>
-   *           &lt;/element>
-   *           &lt;element name="gap">
-   *             &lt;complexType>
-   *               &lt;complexContent>
-   *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                   &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                   &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                   &lt;attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                   &lt;attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *                 &lt;/restriction>
-   *               &lt;/complexContent>
-   *             &lt;/complexType>
-   *           &lt;/element>
-   *         &lt;/choice>
-   *       &lt;/sequence>
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "rangeOrGap" })
-  public static class Contig
-  {
-
-    @XmlElements({
-        @XmlElement(name = "range", type = EntryType.Contig.Range.class),
-        @XmlElement(name = "gap", type = EntryType.Contig.Gap.class) })
-    protected List<Object> rangeOrGap;
+    /**
+     * Sets the value of the comment property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setComment(String value) {
+        this.comment = value;
+    }
 
     /**
-     * Gets the value of the rangeOrGap property.
+     * Gets the value of the keyword property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the rangeOrGap property.
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the keyword property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
-     * 
      * <pre>
-     * getRangeOrGap().add(newItem);
+     *    getKeyword().add(newItem);
      * </pre>
      * 
      * 
      * <p>
      * Objects of the following type(s) are allowed in the list
-     * {@link EntryType.Contig.Range } {@link EntryType.Contig.Gap }
+     * {@link String }
      * 
      * 
      */
-    public List<Object> getRangeOrGap()
-    {
-      if (rangeOrGap == null)
-      {
-        rangeOrGap = new ArrayList<Object>();
-      }
-      return this.rangeOrGap;
+    public List<String> getKeyword() {
+        if (keyword == null) {
+            keyword = new ArrayList<String>();
+        }
+        return this.keyword;
     }
 
     /**
-     * <p>
-     * Java class for anonymous complex type.
+     * Gets the value of the reference property.
      * 
      * <p>
-     * The following schema fragment specifies the expected content contained
-     * within this class.
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the reference property.
      * 
+     * <p>
+     * For example, to add a new item, do as follows:
      * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       &lt;attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       &lt;attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
+     *    getReference().add(newItem);
      * </pre>
      * 
      * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link EntryType.Reference }
+     * 
+     * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class Gap
-    {
-
-      @XmlAttribute(name = "begin", required = true)
-      protected BigInteger begin;
-
-      @XmlAttribute(name = "end", required = true)
-      protected BigInteger end;
-
-      @XmlAttribute(name = "length", required = true)
-      protected BigInteger length;
-
-      @XmlAttribute(name = "unknownLength")
-      protected Boolean unknownLength;
-
-      /**
-       * Gets the value of the begin property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getBegin()
-      {
-        return begin;
-      }
-
-      /**
-       * Sets the value of the begin property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setBegin(BigInteger value)
-      {
-        this.begin = value;
-      }
-
-      /**
-       * Gets the value of the end property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getEnd()
-      {
-        return end;
-      }
-
-      /**
-       * Sets the value of the end property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setEnd(BigInteger value)
-      {
-        this.end = value;
-      }
-
-      /**
-       * Gets the value of the length property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getLength()
-      {
-        return length;
-      }
-
-      /**
-       * Sets the value of the length property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setLength(BigInteger value)
-      {
-        this.length = value;
-      }
-
-      /**
-       * Gets the value of the unknownLength property.
-       * 
-       * @return possible object is {@link Boolean }
-       * 
-       */
-      public boolean isUnknownLength()
-      {
-        if (unknownLength == null)
-        {
-          return false;
+    public List<EntryType.Reference> getReference() {
+        if (reference == null) {
+            reference = new ArrayList<EntryType.Reference>();
         }
-        else
-        {
-          return unknownLength;
-        }
-      }
-
-      /**
-       * Sets the value of the unknownLength property.
-       * 
-       * @param value
-       *          allowed object is {@link Boolean }
-       * 
-       */
-      public void setUnknownLength(Boolean value)
-      {
-        this.unknownLength = value;
-      }
-
+        return this.reference;
     }
 
     /**
-     * <p>
-     * Java class for anonymous complex type.
+     * Gets the value of the xref property.
      * 
      * <p>
-     * The following schema fragment specifies the expected content contained
-     * within this class.
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the xref property.
      * 
+     * <p>
+     * For example, to add a new item, do as follows:
      * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
+     *    getXref().add(newItem);
      * </pre>
      * 
      * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link XrefType }
+     * 
+     * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class Range
-    {
-
-      @XmlAttribute(name = "begin", required = true)
-      protected BigInteger begin;
-
-      @XmlAttribute(name = "end", required = true)
-      protected BigInteger end;
-
-      @XmlAttribute(name = "primaryBegin")
-      protected BigInteger primaryBegin;
-
-      @XmlAttribute(name = "primaryEnd")
-      protected BigInteger primaryEnd;
-
-      @XmlAttribute(name = "accession", required = true)
-      protected String accession;
-
-      @XmlAttribute(name = "version", required = true)
-      protected BigInteger version;
-
-      @XmlAttribute(name = "complement")
-      protected Boolean complement;
-
-      /**
-       * Gets the value of the begin property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getBegin()
-      {
-        return begin;
-      }
-
-      /**
-       * Sets the value of the begin property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setBegin(BigInteger value)
-      {
-        this.begin = value;
-      }
-
-      /**
-       * Gets the value of the end property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getEnd()
-      {
-        return end;
-      }
-
-      /**
-       * Sets the value of the end property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setEnd(BigInteger value)
-      {
-        this.end = value;
-      }
-
-      /**
-       * Gets the value of the primaryBegin property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getPrimaryBegin()
-      {
-        return primaryBegin;
-      }
-
-      /**
-       * Sets the value of the primaryBegin property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setPrimaryBegin(BigInteger value)
-      {
-        this.primaryBegin = value;
-      }
-
-      /**
-       * Gets the value of the primaryEnd property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getPrimaryEnd()
-      {
-        return primaryEnd;
-      }
-
-      /**
-       * Sets the value of the primaryEnd property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setPrimaryEnd(BigInteger value)
-      {
-        this.primaryEnd = value;
-      }
-
-      /**
-       * Gets the value of the accession property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getAccession()
-      {
-        return accession;
-      }
-
-      /**
-       * Sets the value of the accession property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setAccession(String value)
-      {
-        this.accession = value;
-      }
-
-      /**
-       * Gets the value of the version property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getVersion()
-      {
-        return version;
-      }
-
-      /**
-       * Sets the value of the version property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setVersion(BigInteger value)
-      {
-        this.version = value;
-      }
-
-      /**
-       * Gets the value of the complement property.
-       * 
-       * @return possible object is {@link Boolean }
-       * 
-       */
-      public boolean isComplement()
-      {
-        if (complement == null)
-        {
-          return false;
-        }
-        else
-        {
-          return complement;
+    public List<XrefType> getXref() {
+        if (xref == null) {
+            xref = new ArrayList<XrefType>();
         }
-      }
-
-      /**
-       * Sets the value of the complement property.
-       * 
-       * @param value
-       *          allowed object is {@link Boolean }
-       * 
-       */
-      public void setComplement(Boolean value)
-      {
-        this.complement = value;
-      }
-
+        return this.xref;
     }
 
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;sequence>
-   *         &lt;element name="taxon" minOccurs="0">
-   *           &lt;complexType>
-   *             &lt;complexContent>
-   *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 &lt;sequence>
-   *                   &lt;element name="lineage" minOccurs="0">
-   *                     &lt;complexType>
-   *                       &lt;complexContent>
-   *                         &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                           &lt;sequence>
-   *                             &lt;element name="taxon" maxOccurs="unbounded">
-   *                               &lt;complexType>
-   *                                 &lt;complexContent>
-   *                                   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                                     &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                                   &lt;/restriction>
-   *                                 &lt;/complexContent>
-   *                               &lt;/complexType>
-   *                             &lt;/element>
-   *                           &lt;/sequence>
-   *                         &lt;/restriction>
-   *                       &lt;/complexContent>
-   *                     &lt;/complexType>
-   *                   &lt;/element>
-   *                 &lt;/sequence>
-   *                 &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 &lt;attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 &lt;attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *               &lt;/restriction>
-   *             &lt;/complexContent>
-   *           &lt;/complexType>
-   *         &lt;/element>
-   *         &lt;element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
-   *         &lt;element name="qualifier" maxOccurs="unbounded" minOccurs="0">
-   *           &lt;complexType>
-   *             &lt;complexContent>
-   *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 &lt;sequence>
-   *                   &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-   *                 &lt;/sequence>
-   *                 &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *               &lt;/restriction>
-   *             &lt;/complexContent>
-   *           &lt;/complexType>
-   *         &lt;/element>
-   *       &lt;/sequence>
-   *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       &lt;attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "taxon", "xref", "qualifier" })
-  public static class Feature
-  {
-
-    protected EntryType.Feature.FeatureTaxon taxon;
-
-    protected List<XrefType> xref;
+    /**
+     * Gets the value of the feature property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the feature property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getFeature().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link EntryType.Feature }
+     * 
+     * 
+     */
+    public List<EntryType.Feature> getFeature() {
+        if (feature == null) {
+            feature = new ArrayList<EntryType.Feature>();
+        }
+        return this.feature;
+    }
 
-    protected List<EntryType.Feature.Qualifier> qualifier;
+    /**
+     * Gets the value of the assembly property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link EntryType.Assembly }
+     *     
+     */
+    public EntryType.Assembly getAssembly() {
+        return assembly;
+    }
 
-    @XmlAttribute(name = "name", required = true)
-    protected String name;
+    /**
+     * Sets the value of the assembly property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link EntryType.Assembly }
+     *     
+     */
+    public void setAssembly(EntryType.Assembly value) {
+        this.assembly = value;
+    }
 
-    @XmlAttribute(name = "location", required = true)
-    protected String location;
+    /**
+     * Gets the value of the contig property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link EntryType.Contig }
+     *     
+     */
+    public EntryType.Contig getContig() {
+        return contig;
+    }
 
     /**
-     * Gets the value of the taxon property.
+     * Sets the value of the contig property.
      * 
-     * @return possible object is {@link EntryType.Feature.FeatureTaxon }
+     * @param value
+     *     allowed object is
+     *     {@link EntryType.Contig }
+     *     
+     */
+    public void setContig(EntryType.Contig value) {
+        this.contig = value;
+    }
+
+    /**
+     * Gets the value of the sequence property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public EntryType.Feature.FeatureTaxon getTaxon()
-    {
-      return taxon;
+    public String getSequence() {
+        return sequence;
     }
 
     /**
-     * Sets the value of the taxon property.
+     * Sets the value of the sequence property.
      * 
      * @param value
-     *          allowed object is {@link EntryType.Feature.FeatureTaxon }
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setSequence(String value) {
+        this.sequence = value;
+    }
+
+    /**
+     * Gets the value of the accession property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public void setTaxon(EntryType.Feature.FeatureTaxon value)
-    {
-      this.taxon = value;
+    public String getAccession() {
+        return accession;
     }
 
     /**
-     * Gets the value of the xref property.
+     * Sets the value of the accession property.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the xref property.
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setAccession(String value) {
+        this.accession = value;
+    }
+
+    /**
+     * Gets the value of the version property.
      * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * @return
+     *     possible object is
+     *     {@link BigInteger }
+     *     
+     */
+    public BigInteger getVersion() {
+        return version;
+    }
+
+    /**
+     * Sets the value of the version property.
      * 
-     * <pre>
-     * getXref().add(newItem);
-     * </pre>
+     * @param value
+     *     allowed object is
+     *     {@link BigInteger }
+     *     
+     */
+    public void setVersion(BigInteger value) {
+        this.version = value;
+    }
+
+    /**
+     * Gets the value of the entryVersion property.
      * 
+     * @return
+     *     possible object is
+     *     {@link BigInteger }
+     *     
+     */
+    public BigInteger getEntryVersion() {
+        return entryVersion;
+    }
+
+    /**
+     * Sets the value of the entryVersion property.
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list {@link XrefType
-     * }
+     * @param value
+     *     allowed object is
+     *     {@link BigInteger }
+     *     
+     */
+    public void setEntryVersion(BigInteger value) {
+        this.entryVersion = value;
+    }
+
+    /**
+     * Gets the value of the dataClass property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDataClass() {
+        return dataClass;
+    }
+
+    /**
+     * Sets the value of the dataClass property.
      * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public List<XrefType> getXref()
-    {
-      if (xref == null)
-      {
-        xref = new ArrayList<XrefType>();
-      }
-      return this.xref;
+    public void setDataClass(String value) {
+        this.dataClass = value;
     }
 
     /**
-     * Gets the value of the qualifier property.
+     * Gets the value of the taxonomicDivision property.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the qualifier property.
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getTaxonomicDivision() {
+        return taxonomicDivision;
+    }
+
+    /**
+     * Sets the value of the taxonomicDivision property.
      * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setTaxonomicDivision(String value) {
+        this.taxonomicDivision = value;
+    }
+
+    /**
+     * Gets the value of the moleculeType property.
      * 
-     * <pre>
-     * getQualifier().add(newItem);
-     * </pre>
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getMoleculeType() {
+        return moleculeType;
+    }
+
+    /**
+     * Sets the value of the moleculeType property.
      * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setMoleculeType(String value) {
+        this.moleculeType = value;
+    }
+
+    /**
+     * Gets the value of the sequenceLength property.
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link EntryType.Feature.Qualifier }
+     * @return
+     *     possible object is
+     *     {@link BigInteger }
+     *     
+     */
+    public BigInteger getSequenceLength() {
+        return sequenceLength;
+    }
+
+    /**
+     * Sets the value of the sequenceLength property.
      * 
+     * @param value
+     *     allowed object is
+     *     {@link BigInteger }
+     *     
+     */
+    public void setSequenceLength(BigInteger value) {
+        this.sequenceLength = value;
+    }
+
+    /**
+     * Gets the value of the topology property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public List<EntryType.Feature.Qualifier> getQualifier()
-    {
-      if (qualifier == null)
-      {
-        qualifier = new ArrayList<EntryType.Feature.Qualifier>();
-      }
-      return this.qualifier;
+    public String getTopology() {
+        return topology;
     }
 
     /**
-     * Gets the value of the name property.
+     * Sets the value of the topology property.
      * 
-     * @return possible object is {@link String }
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setTopology(String value) {
+        this.topology = value;
+    }
+
+    /**
+     * Gets the value of the firstPublic property.
      * 
+     * @return
+     *     possible object is
+     *     {@link XMLGregorianCalendar }
+     *     
      */
-    public String getName()
-    {
-      return name;
+    public XMLGregorianCalendar getFirstPublic() {
+        return firstPublic;
     }
 
     /**
-     * Sets the value of the name property.
+     * Sets the value of the firstPublic property.
      * 
      * @param value
-     *          allowed object is {@link String }
+     *     allowed object is
+     *     {@link XMLGregorianCalendar }
+     *     
+     */
+    public void setFirstPublic(XMLGregorianCalendar value) {
+        this.firstPublic = value;
+    }
+
+    /**
+     * Gets the value of the firstPublicRelease property.
      * 
+     * @return
+     *     possible object is
+     *     {@link BigInteger }
+     *     
      */
-    public void setName(String value)
-    {
-      this.name = value;
+    public BigInteger getFirstPublicRelease() {
+        return firstPublicRelease;
     }
 
     /**
-     * Gets the value of the location property.
+     * Sets the value of the firstPublicRelease property.
      * 
-     * @return possible object is {@link String }
+     * @param value
+     *     allowed object is
+     *     {@link BigInteger }
+     *     
+     */
+    public void setFirstPublicRelease(BigInteger value) {
+        this.firstPublicRelease = value;
+    }
+
+    /**
+     * Gets the value of the lastUpdated property.
      * 
+     * @return
+     *     possible object is
+     *     {@link XMLGregorianCalendar }
+     *     
      */
-    public String getLocation()
-    {
-      return location;
+    public XMLGregorianCalendar getLastUpdated() {
+        return lastUpdated;
     }
 
     /**
-     * Sets the value of the location property.
+     * Sets the value of the lastUpdated property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link XMLGregorianCalendar }
+     *     
      */
-    public void setLocation(String value)
-    {
-      this.location = value;
+    public void setLastUpdated(XMLGregorianCalendar value) {
+        this.lastUpdated = value;
     }
 
     /**
-     * <p>
-     * Java class for anonymous complex type.
+     * Gets the value of the lastUpdatedRelease property.
      * 
-     * <p>
-     * The following schema fragment specifies the expected content contained
-     * within this class.
+     * @return
+     *     possible object is
+     *     {@link BigInteger }
+     *     
+     */
+    public BigInteger getLastUpdatedRelease() {
+        return lastUpdatedRelease;
+    }
+
+    /**
+     * Sets the value of the lastUpdatedRelease property.
      * 
-     * <pre>
-     * &lt;complexType>
+     * @param value
+     *     allowed object is
+     *     {@link BigInteger }
+     *     
+     */
+    public void setLastUpdatedRelease(BigInteger value) {
+        this.lastUpdatedRelease = value;
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
      *   &lt;complexContent>
      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
      *       &lt;sequence>
-     *         &lt;element name="lineage" minOccurs="0">
+     *         &lt;element name="range" maxOccurs="unbounded">
      *           &lt;complexType>
      *             &lt;complexContent>
      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;sequence>
-     *                   &lt;element name="taxon" maxOccurs="unbounded">
-     *                     &lt;complexType>
-     *                       &lt;complexContent>
-     *                         &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                           &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                         &lt;/restriction>
-     *                       &lt;/complexContent>
-     *                     &lt;/complexType>
-     *                   &lt;/element>
-     *                 &lt;/sequence>
+     *                 &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                 &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                 &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                 &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                 &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                 &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
      *               &lt;/restriction>
      *             &lt;/complexContent>
      *           &lt;/complexType>
      *         &lt;/element>
      *       &lt;/sequence>
-     *       &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
      *     &lt;/restriction>
      *   &lt;/complexContent>
      * &lt;/complexType>
@@ -1894,198 +896,366 @@ public class EntryType
      * 
      */
     @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = { "lineage" })
-    public static class FeatureTaxon
-    {
-
-      protected EntryType.Feature.FeatureTaxon.Lineage lineage;
-
-      @XmlAttribute(name = "scientificName", required = true)
-      protected String scientificName;
-
-      @XmlAttribute(name = "commonName")
-      protected String commonName;
-
-      @XmlAttribute(name = "taxId")
-      protected BigInteger taxId;
-
-      /**
-       * Gets the value of the lineage property.
-       * 
-       * @return possible object is
-       *         {@link EntryType.Feature.FeatureTaxon.Lineage }
-       * 
-       */
-      public EntryType.Feature.FeatureTaxon.Lineage getLineage()
-      {
-        return lineage;
-      }
-
-      /**
-       * Sets the value of the lineage property.
-       * 
-       * @param value
-       *          allowed object is
-       *          {@link EntryType.Feature.FeatureTaxon.Lineage }
-       * 
-       */
-      public void setLineage(EntryType.Feature.FeatureTaxon.Lineage value)
-      {
-        this.lineage = value;
-      }
-
-      /**
-       * Gets the value of the scientificName property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getScientificName()
-      {
-        return scientificName;
-      }
-
-      /**
-       * Sets the value of the scientificName property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setScientificName(String value)
-      {
-        this.scientificName = value;
-      }
-
-      /**
-       * Gets the value of the commonName property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getCommonName()
-      {
-        return commonName;
-      }
-
-      /**
-       * Sets the value of the commonName property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setCommonName(String value)
-      {
-        this.commonName = value;
-      }
-
-      /**
-       * Gets the value of the taxId property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getTaxId()
-      {
-        return taxId;
-      }
-
-      /**
-       * Sets the value of the taxId property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setTaxId(BigInteger value)
-      {
-        this.taxId = value;
-      }
-
-      /**
-       * <p>
-       * Java class for anonymous complex type.
-       * 
-       * <p>
-       * The following schema fragment specifies the expected content contained
-       * within this class.
-       * 
-       * <pre>
-       * &lt;complexType>
-       *   &lt;complexContent>
-       *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-       *       &lt;sequence>
-       *         &lt;element name="taxon" maxOccurs="unbounded">
-       *           &lt;complexType>
-       *             &lt;complexContent>
-       *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-       *                 &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *               &lt;/restriction>
-       *             &lt;/complexContent>
-       *           &lt;/complexType>
-       *         &lt;/element>
-       *       &lt;/sequence>
-       *     &lt;/restriction>
-       *   &lt;/complexContent>
-       * &lt;/complexType>
-       * </pre>
-       * 
-       * 
-       */
-      @XmlAccessorType(XmlAccessType.FIELD)
-      @XmlType(name = "", propOrder = { "taxon" })
-      public static class Lineage
-      {
+    @XmlType(name = "", propOrder = {
+        "range"
+    })
+    public static class Assembly {
 
         @XmlElement(required = true)
-        protected List<EntryType.Feature.FeatureTaxon.Lineage.Taxon> taxon;
+        protected List<EntryType.Assembly.Range> range;
 
         /**
-         * Gets the value of the taxon property.
+         * Gets the value of the range property.
          * 
          * <p>
-         * This accessor method returns a reference to the live list, not a
-         * snapshot. Therefore any modification you make to the returned list
-         * will be present inside the JAXB object. This is why there is not a
-         * <CODE>set</CODE> method for the taxon property.
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the range property.
          * 
          * <p>
          * For example, to add a new item, do as follows:
-         * 
          * <pre>
-         * getTaxon().add(newItem);
+         *    getRange().add(newItem);
          * </pre>
          * 
          * 
          * <p>
          * Objects of the following type(s) are allowed in the list
-         * {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
+         * {@link EntryType.Assembly.Range }
+         * 
+         * 
+         */
+        public List<EntryType.Assembly.Range> getRange() {
+            if (range == null) {
+                range = new ArrayList<EntryType.Assembly.Range>();
+            }
+            return this.range;
+        }
+
+
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+         *     &lt;/restriction>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
          * 
          * 
          */
-        public List<EntryType.Feature.FeatureTaxon.Lineage.Taxon> getTaxon()
-        {
-          if (taxon == null)
-          {
-            taxon = new ArrayList<EntryType.Feature.FeatureTaxon.Lineage.Taxon>();
-          }
-          return this.taxon;
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class Range {
+
+            @XmlAttribute(name = "begin", required = true)
+            protected BigInteger begin;
+            @XmlAttribute(name = "end", required = true)
+            protected BigInteger end;
+            @XmlAttribute(name = "primaryBegin")
+            protected BigInteger primaryBegin;
+            @XmlAttribute(name = "primaryEnd")
+            protected BigInteger primaryEnd;
+            @XmlAttribute(name = "accession", required = true)
+            protected String accession;
+            @XmlAttribute(name = "version", required = true)
+            protected BigInteger version;
+            @XmlAttribute(name = "complement")
+            protected Boolean complement;
+
+            /**
+             * Gets the value of the begin property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getBegin() {
+                return begin;
+            }
+
+            /**
+             * Sets the value of the begin property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setBegin(BigInteger value) {
+                this.begin = value;
+            }
+
+            /**
+             * Gets the value of the end property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getEnd() {
+                return end;
+            }
+
+            /**
+             * Sets the value of the end property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setEnd(BigInteger value) {
+                this.end = value;
+            }
+
+            /**
+             * Gets the value of the primaryBegin property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getPrimaryBegin() {
+                return primaryBegin;
+            }
+
+            /**
+             * Sets the value of the primaryBegin property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setPrimaryBegin(BigInteger value) {
+                this.primaryBegin = value;
+            }
+
+            /**
+             * Gets the value of the primaryEnd property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getPrimaryEnd() {
+                return primaryEnd;
+            }
+
+            /**
+             * Sets the value of the primaryEnd property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setPrimaryEnd(BigInteger value) {
+                this.primaryEnd = value;
+            }
+
+            /**
+             * Gets the value of the accession property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getAccession() {
+                return accession;
+            }
+
+            /**
+             * Sets the value of the accession property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setAccession(String value) {
+                this.accession = value;
+            }
+
+            /**
+             * Gets the value of the version property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getVersion() {
+                return version;
+            }
+
+            /**
+             * Sets the value of the version property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setVersion(BigInteger value) {
+                this.version = value;
+            }
+
+            /**
+             * Gets the value of the complement property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Boolean }
+             *     
+             */
+            public boolean isComplement() {
+                if (complement == null) {
+                    return false;
+                } else {
+                    return complement;
+                }
+            }
+
+            /**
+             * Sets the value of the complement property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Boolean }
+             *     
+             */
+            public void setComplement(Boolean value) {
+                this.complement = value;
+            }
+
         }
 
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;choice maxOccurs="unbounded" minOccurs="0">
+     *           &lt;element name="range">
+     *             &lt;complexType>
+     *               &lt;complexContent>
+     *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                   &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                   &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                   &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                   &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                   &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                   &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                   &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *                 &lt;/restriction>
+     *               &lt;/complexContent>
+     *             &lt;/complexType>
+     *           &lt;/element>
+     *           &lt;element name="gap">
+     *             &lt;complexType>
+     *               &lt;complexContent>
+     *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                   &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                   &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                   &lt;attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                   &lt;attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *                 &lt;/restriction>
+     *               &lt;/complexContent>
+     *             &lt;/complexType>
+     *           &lt;/element>
+     *         &lt;/choice>
+     *       &lt;/sequence>
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "rangeOrGap"
+    })
+    public static class Contig {
+
+        @XmlElements({
+            @XmlElement(name = "range", type = EntryType.Contig.Range.class),
+            @XmlElement(name = "gap", type = EntryType.Contig.Gap.class)
+        })
+        protected List<Object> rangeOrGap;
+
         /**
+         * Gets the value of the rangeOrGap property.
+         * 
          * <p>
-         * Java class for anonymous complex type.
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the rangeOrGap property.
          * 
          * <p>
-         * The following schema fragment specifies the expected content
-         * contained within this class.
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getRangeOrGap().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link EntryType.Contig.Range }
+         * {@link EntryType.Contig.Gap }
+         * 
+         * 
+         */
+        public List<Object> getRangeOrGap() {
+            if (rangeOrGap == null) {
+                rangeOrGap = new ArrayList<Object>();
+            }
+            return this.rangeOrGap;
+        }
+
+
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
          * 
          * <pre>
          * &lt;complexType>
          *   &lt;complexContent>
          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       &lt;attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       &lt;attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
          *     &lt;/restriction>
          *   &lt;/complexContent>
          * &lt;/complexType>
@@ -2095,57 +1265,397 @@ public class EntryType
          */
         @XmlAccessorType(XmlAccessType.FIELD)
         @XmlType(name = "")
-        public static class Taxon
-        {
-
-          @XmlAttribute(name = "scientificName", required = true)
-          protected String scientificName;
-
-          /**
-           * Gets the value of the scientificName property.
-           * 
-           * @return possible object is {@link String }
-           * 
-           */
-          public String getScientificName()
-          {
-            return scientificName;
-          }
-
-          /**
-           * Sets the value of the scientificName property.
-           * 
-           * @param value
-           *          allowed object is {@link String }
-           * 
-           */
-          public void setScientificName(String value)
-          {
-            this.scientificName = value;
-          }
+        public static class Gap {
+
+            @XmlAttribute(name = "begin", required = true)
+            protected BigInteger begin;
+            @XmlAttribute(name = "end", required = true)
+            protected BigInteger end;
+            @XmlAttribute(name = "length", required = true)
+            protected BigInteger length;
+            @XmlAttribute(name = "unknownLength")
+            protected Boolean unknownLength;
+
+            /**
+             * Gets the value of the begin property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getBegin() {
+                return begin;
+            }
+
+            /**
+             * Sets the value of the begin property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setBegin(BigInteger value) {
+                this.begin = value;
+            }
+
+            /**
+             * Gets the value of the end property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getEnd() {
+                return end;
+            }
+
+            /**
+             * Sets the value of the end property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setEnd(BigInteger value) {
+                this.end = value;
+            }
+
+            /**
+             * Gets the value of the length property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getLength() {
+                return length;
+            }
+
+            /**
+             * Sets the value of the length property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setLength(BigInteger value) {
+                this.length = value;
+            }
+
+            /**
+             * Gets the value of the unknownLength property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Boolean }
+             *     
+             */
+            public boolean isUnknownLength() {
+                if (unknownLength == null) {
+                    return false;
+                } else {
+                    return unknownLength;
+                }
+            }
+
+            /**
+             * Sets the value of the unknownLength property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Boolean }
+             *     
+             */
+            public void setUnknownLength(Boolean value) {
+                this.unknownLength = value;
+            }
 
         }
 
-      }
+
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+         *     &lt;/restriction>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class Range {
+
+            @XmlAttribute(name = "begin", required = true)
+            protected BigInteger begin;
+            @XmlAttribute(name = "end", required = true)
+            protected BigInteger end;
+            @XmlAttribute(name = "primaryBegin")
+            protected BigInteger primaryBegin;
+            @XmlAttribute(name = "primaryEnd")
+            protected BigInteger primaryEnd;
+            @XmlAttribute(name = "accession", required = true)
+            protected String accession;
+            @XmlAttribute(name = "version", required = true)
+            protected BigInteger version;
+            @XmlAttribute(name = "complement")
+            protected Boolean complement;
+
+            /**
+             * Gets the value of the begin property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getBegin() {
+                return begin;
+            }
+
+            /**
+             * Sets the value of the begin property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setBegin(BigInteger value) {
+                this.begin = value;
+            }
+
+            /**
+             * Gets the value of the end property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getEnd() {
+                return end;
+            }
+
+            /**
+             * Sets the value of the end property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setEnd(BigInteger value) {
+                this.end = value;
+            }
+
+            /**
+             * Gets the value of the primaryBegin property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getPrimaryBegin() {
+                return primaryBegin;
+            }
+
+            /**
+             * Sets the value of the primaryBegin property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setPrimaryBegin(BigInteger value) {
+                this.primaryBegin = value;
+            }
+
+            /**
+             * Gets the value of the primaryEnd property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getPrimaryEnd() {
+                return primaryEnd;
+            }
+
+            /**
+             * Sets the value of the primaryEnd property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setPrimaryEnd(BigInteger value) {
+                this.primaryEnd = value;
+            }
+
+            /**
+             * Gets the value of the accession property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getAccession() {
+                return accession;
+            }
+
+            /**
+             * Sets the value of the accession property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setAccession(String value) {
+                this.accession = value;
+            }
+
+            /**
+             * Gets the value of the version property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getVersion() {
+                return version;
+            }
+
+            /**
+             * Sets the value of the version property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setVersion(BigInteger value) {
+                this.version = value;
+            }
+
+            /**
+             * Gets the value of the complement property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Boolean }
+             *     
+             */
+            public boolean isComplement() {
+                if (complement == null) {
+                    return false;
+                } else {
+                    return complement;
+                }
+            }
+
+            /**
+             * Sets the value of the complement property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Boolean }
+             *     
+             */
+            public void setComplement(Boolean value) {
+                this.complement = value;
+            }
+
+        }
 
     }
 
+
     /**
-     * <p>
-     * Java class for anonymous complex type.
+     * <p>Java class for anonymous complex type.
      * 
-     * <p>
-     * The following schema fragment specifies the expected content contained
-     * within this class.
+     * <p>The following schema fragment specifies the expected content contained within this class.
      * 
      * <pre>
      * &lt;complexType>
      *   &lt;complexContent>
      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
      *       &lt;sequence>
-     *         &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+     *         &lt;element name="taxon" minOccurs="0">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 &lt;sequence>
+     *                   &lt;element name="lineage" minOccurs="0">
+     *                     &lt;complexType>
+     *                       &lt;complexContent>
+     *                         &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                           &lt;sequence>
+     *                             &lt;element name="taxon" maxOccurs="unbounded">
+     *                               &lt;complexType>
+     *                                 &lt;complexContent>
+     *                                   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                                     &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                                   &lt;/restriction>
+     *                                 &lt;/complexContent>
+     *                               &lt;/complexType>
+     *                             &lt;/element>
+     *                           &lt;/sequence>
+     *                         &lt;/restriction>
+     *                       &lt;/complexContent>
+     *                     &lt;/complexType>
+     *                   &lt;/element>
+     *                 &lt;/sequence>
+     *                 &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 &lt;attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 &lt;attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *               &lt;/restriction>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *         &lt;element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+     *         &lt;element name="qualifier" maxOccurs="unbounded" minOccurs="0">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 &lt;sequence>
+     *                   &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+     *                 &lt;/sequence>
+     *                 &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *               &lt;/restriction>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
      *       &lt;/sequence>
      *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
      *     &lt;/restriction>
      *   &lt;/complexContent>
      * &lt;/complexType>
@@ -2154,578 +1664,1017 @@ public class EntryType
      * 
      */
     @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = { "value" })
-    public static class Qualifier
-    {
-
-      protected String value;
-
-      @XmlAttribute(name = "name", required = true)
-      protected String name;
-
-      /**
-       * Gets the value of the value property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getValue()
-      {
-        return value;
-      }
-
-      /**
-       * Sets the value of the value property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setValue(String value)
-      {
-        this.value = value;
-      }
-
-      /**
-       * Gets the value of the name property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getName()
-      {
-        return name;
-      }
-
-      /**
-       * Sets the value of the name property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setName(String value)
-      {
-        this.name = value;
-      }
-
-    }
+    @XmlType(name = "", propOrder = {
+        "taxon",
+        "xref",
+        "qualifier"
+    })
+    public static class Feature {
+
+        protected EntryType.Feature.FeatureTaxon taxon;
+        protected List<XrefType> xref;
+        protected List<EntryType.Feature.Qualifier> qualifier;
+        @XmlAttribute(name = "name", required = true)
+        protected String name;
+        @XmlAttribute(name = "location", required = true)
+        protected String location;
 
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;sequence>
-   *         &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-   *         &lt;element name="author" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
-   *         &lt;element name="applicant" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
-   *         &lt;element name="consortium" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-   *         &lt;element name="submissionDate" type="{http://www.w3.org/2001/XMLSchema}date" minOccurs="0"/>
-   *         &lt;element name="journal" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-   *         &lt;element name="year" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-   *         &lt;element name="volume" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-   *         &lt;element name="issue" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-   *         &lt;element name="firstPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-   *         &lt;element name="lastPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-   *         &lt;element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-   *         &lt;element name="referenceLocation" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-   *         &lt;element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
-   *       &lt;/sequence>
-   *       &lt;attribute name="type" use="required">
-   *         &lt;simpleType>
-   *           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
-   *             &lt;enumeration value="submission"/>
-   *             &lt;enumeration value="book"/>
-   *             &lt;enumeration value="article"/>
-   *             &lt;enumeration value="patent"/>
-   *             &lt;enumeration value="thesis"/>
-   *             &lt;enumeration value="unpublished"/>
-   *           &lt;/restriction>
-   *         &lt;/simpleType>
-   *       &lt;/attribute>
-   *       &lt;attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *       &lt;attribute name="location" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(
-    name = "",
-    propOrder =
-    { "title", "author", "applicant", "consortium", "submissionDate",
-        "journal", "year", "volume", "issue", "firstPage", "lastPage",
-        "comment", "referenceLocation", "xref" })
-  public static class Reference
-  {
-
-    protected String title;
-
-    protected List<String> author;
-
-    protected List<String> applicant;
-
-    protected String consortium;
+        /**
+         * Gets the value of the taxon property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link EntryType.Feature.FeatureTaxon }
+         *     
+         */
+        public EntryType.Feature.FeatureTaxon getTaxon() {
+            return taxon;
+        }
 
-    @XmlSchemaType(name = "date")
-    protected XMLGregorianCalendar submissionDate;
+        /**
+         * Sets the value of the taxon property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link EntryType.Feature.FeatureTaxon }
+         *     
+         */
+        public void setTaxon(EntryType.Feature.FeatureTaxon value) {
+            this.taxon = value;
+        }
 
-    protected String journal;
+        /**
+         * Gets the value of the xref property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the xref property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getXref().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link XrefType }
+         * 
+         * 
+         */
+        public List<XrefType> getXref() {
+            if (xref == null) {
+                xref = new ArrayList<XrefType>();
+            }
+            return this.xref;
+        }
 
-    protected String year;
+        /**
+         * Gets the value of the qualifier property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the qualifier property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getQualifier().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link EntryType.Feature.Qualifier }
+         * 
+         * 
+         */
+        public List<EntryType.Feature.Qualifier> getQualifier() {
+            if (qualifier == null) {
+                qualifier = new ArrayList<EntryType.Feature.Qualifier>();
+            }
+            return this.qualifier;
+        }
 
-    protected String volume;
+        /**
+         * Gets the value of the name property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getName() {
+            return name;
+        }
 
-    protected String issue;
+        /**
+         * Sets the value of the name property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setName(String value) {
+            this.name = value;
+        }
 
-    protected String firstPage;
+        /**
+         * Gets the value of the location property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getLocation() {
+            return location;
+        }
 
-    protected String lastPage;
+        /**
+         * Sets the value of the location property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setLocation(String value) {
+            this.location = value;
+        }
 
-    protected String comment;
 
-    protected String referenceLocation;
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       &lt;sequence>
+         *         &lt;element name="lineage" minOccurs="0">
+         *           &lt;complexType>
+         *             &lt;complexContent>
+         *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *                 &lt;sequence>
+         *                   &lt;element name="taxon" maxOccurs="unbounded">
+         *                     &lt;complexType>
+         *                       &lt;complexContent>
+         *                         &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *                           &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *                         &lt;/restriction>
+         *                       &lt;/complexContent>
+         *                     &lt;/complexType>
+         *                   &lt;/element>
+         *                 &lt;/sequence>
+         *               &lt;/restriction>
+         *             &lt;/complexContent>
+         *           &lt;/complexType>
+         *         &lt;/element>
+         *       &lt;/sequence>
+         *       &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       &lt;attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       &lt;attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *     &lt;/restriction>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "", propOrder = {
+            "lineage"
+        })
+        public static class FeatureTaxon {
+
+            protected EntryType.Feature.FeatureTaxon.Lineage lineage;
+            @XmlAttribute(name = "scientificName", required = true)
+            protected String scientificName;
+            @XmlAttribute(name = "commonName")
+            protected String commonName;
+            @XmlAttribute(name = "taxId")
+            protected BigInteger taxId;
+
+            /**
+             * Gets the value of the lineage property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link EntryType.Feature.FeatureTaxon.Lineage }
+             *     
+             */
+            public EntryType.Feature.FeatureTaxon.Lineage getLineage() {
+                return lineage;
+            }
+
+            /**
+             * Sets the value of the lineage property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link EntryType.Feature.FeatureTaxon.Lineage }
+             *     
+             */
+            public void setLineage(EntryType.Feature.FeatureTaxon.Lineage value) {
+                this.lineage = value;
+            }
+
+            /**
+             * Gets the value of the scientificName property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getScientificName() {
+                return scientificName;
+            }
+
+            /**
+             * Sets the value of the scientificName property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setScientificName(String value) {
+                this.scientificName = value;
+            }
+
+            /**
+             * Gets the value of the commonName property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getCommonName() {
+                return commonName;
+            }
+
+            /**
+             * Sets the value of the commonName property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setCommonName(String value) {
+                this.commonName = value;
+            }
+
+            /**
+             * Gets the value of the taxId property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getTaxId() {
+                return taxId;
+            }
+
+            /**
+             * Sets the value of the taxId property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setTaxId(BigInteger value) {
+                this.taxId = value;
+            }
+
+
+            /**
+             * <p>Java class for anonymous complex type.
+             * 
+             * <p>The following schema fragment specifies the expected content contained within this class.
+             * 
+             * <pre>
+             * &lt;complexType>
+             *   &lt;complexContent>
+             *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+             *       &lt;sequence>
+             *         &lt;element name="taxon" maxOccurs="unbounded">
+             *           &lt;complexType>
+             *             &lt;complexContent>
+             *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+             *                 &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *               &lt;/restriction>
+             *             &lt;/complexContent>
+             *           &lt;/complexType>
+             *         &lt;/element>
+             *       &lt;/sequence>
+             *     &lt;/restriction>
+             *   &lt;/complexContent>
+             * &lt;/complexType>
+             * </pre>
+             * 
+             * 
+             */
+            @XmlAccessorType(XmlAccessType.FIELD)
+            @XmlType(name = "", propOrder = {
+                "taxon"
+            })
+            public static class Lineage {
+
+                @XmlElement(required = true)
+                protected List<EntryType.Feature.FeatureTaxon.Lineage.Taxon> taxon;
+
+                /**
+                 * Gets the value of the taxon property.
+                 * 
+                 * <p>
+                 * This accessor method returns a reference to the live list,
+                 * not a snapshot. Therefore any modification you make to the
+                 * returned list will be present inside the JAXB object.
+                 * This is why there is not a <CODE>set</CODE> method for the taxon property.
+                 * 
+                 * <p>
+                 * For example, to add a new item, do as follows:
+                 * <pre>
+                 *    getTaxon().add(newItem);
+                 * </pre>
+                 * 
+                 * 
+                 * <p>
+                 * Objects of the following type(s) are allowed in the list
+                 * {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
+                 * 
+                 * 
+                 */
+                public List<EntryType.Feature.FeatureTaxon.Lineage.Taxon> getTaxon() {
+                    if (taxon == null) {
+                        taxon = new ArrayList<EntryType.Feature.FeatureTaxon.Lineage.Taxon>();
+                    }
+                    return this.taxon;
+                }
+
+
+                /**
+                 * <p>Java class for anonymous complex type.
+                 * 
+                 * <p>The following schema fragment specifies the expected content contained within this class.
+                 * 
+                 * <pre>
+                 * &lt;complexType>
+                 *   &lt;complexContent>
+                 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+                 *       &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+                 *     &lt;/restriction>
+                 *   &lt;/complexContent>
+                 * &lt;/complexType>
+                 * </pre>
+                 * 
+                 * 
+                 */
+                @XmlAccessorType(XmlAccessType.FIELD)
+                @XmlType(name = "")
+                public static class Taxon {
+
+                    @XmlAttribute(name = "scientificName", required = true)
+                    protected String scientificName;
+
+                    /**
+                     * Gets the value of the scientificName property.
+                     * 
+                     * @return
+                     *     possible object is
+                     *     {@link String }
+                     *     
+                     */
+                    public String getScientificName() {
+                        return scientificName;
+                    }
+
+                    /**
+                     * Sets the value of the scientificName property.
+                     * 
+                     * @param value
+                     *     allowed object is
+                     *     {@link String }
+                     *     
+                     */
+                    public void setScientificName(String value) {
+                        this.scientificName = value;
+                    }
+
+                }
+
+            }
 
-    protected List<XrefType> xref;
+        }
 
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
 
-    @XmlAttribute(name = "number", required = true)
-    protected BigInteger number;
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       &lt;sequence>
+         *         &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+         *       &lt;/sequence>
+         *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *     &lt;/restriction>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "", propOrder = {
+            "value"
+        })
+        public static class Qualifier {
+
+            protected String value;
+            @XmlAttribute(name = "name", required = true)
+            protected String name;
+
+            /**
+             * Gets the value of the value property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getValue() {
+                return value;
+            }
+
+            /**
+             * Sets the value of the value property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setValue(String value) {
+                this.value = value;
+            }
+
+            /**
+             * Gets the value of the name property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getName() {
+                return name;
+            }
+
+            /**
+             * Sets the value of the name property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setName(String value) {
+                this.name = value;
+            }
 
-    @XmlAttribute(name = "location")
-    protected String location;
+        }
 
-    /**
-     * Gets the value of the title property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getTitle()
-    {
-      return title;
     }
 
-    /**
-     * Sets the value of the title property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setTitle(String value)
-    {
-      this.title = value;
-    }
 
     /**
-     * Gets the value of the author property.
+     * <p>Java class for anonymous complex type.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the author property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * <p>The following schema fragment specifies the expected content contained within this class.
      * 
      * <pre>
-     * getAuthor().add(newItem);
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+     *         &lt;element name="author" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+     *         &lt;element name="applicant" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+     *         &lt;element name="consortium" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+     *         &lt;element name="submissionDate" type="{http://www.w3.org/2001/XMLSchema}date" minOccurs="0"/>
+     *         &lt;element name="journal" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+     *         &lt;element name="year" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+     *         &lt;element name="volume" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+     *         &lt;element name="issue" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+     *         &lt;element name="firstPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+     *         &lt;element name="lastPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+     *         &lt;element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+     *         &lt;element name="referenceLocation" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+     *         &lt;element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+     *       &lt;/sequence>
+     *       &lt;attribute name="type" use="required">
+     *         &lt;simpleType>
+     *           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
+     *             &lt;enumeration value="submission"/>
+     *             &lt;enumeration value="book"/>
+     *             &lt;enumeration value="article"/>
+     *             &lt;enumeration value="patent"/>
+     *             &lt;enumeration value="thesis"/>
+     *             &lt;enumeration value="unpublished"/>
+     *           &lt;/restriction>
+     *         &lt;/simpleType>
+     *       &lt;/attribute>
+     *       &lt;attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       &lt;attribute name="location" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
      * </pre>
      * 
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list {@link String }
-     * 
-     * 
      */
-    public List<String> getAuthor()
-    {
-      if (author == null)
-      {
-        author = new ArrayList<String>();
-      }
-      return this.author;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "title",
+        "author",
+        "applicant",
+        "consortium",
+        "submissionDate",
+        "journal",
+        "year",
+        "volume",
+        "issue",
+        "firstPage",
+        "lastPage",
+        "comment",
+        "referenceLocation",
+        "xref"
+    })
+    public static class Reference {
+
+        protected String title;
+        protected List<String> author;
+        protected List<String> applicant;
+        protected String consortium;
+        @XmlSchemaType(name = "date")
+        protected XMLGregorianCalendar submissionDate;
+        protected String journal;
+        protected String year;
+        protected String volume;
+        protected String issue;
+        protected String firstPage;
+        protected String lastPage;
+        protected String comment;
+        protected String referenceLocation;
+        protected List<XrefType> xref;
+        @XmlAttribute(name = "type", required = true)
+        protected String type;
+        @XmlAttribute(name = "number", required = true)
+        protected BigInteger number;
+        @XmlAttribute(name = "location")
+        protected String location;
 
-    /**
-     * Gets the value of the applicant property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the applicant property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * 
-     * <pre>
-     * getApplicant().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list {@link String }
-     * 
-     * 
-     */
-    public List<String> getApplicant()
-    {
-      if (applicant == null)
-      {
-        applicant = new ArrayList<String>();
-      }
-      return this.applicant;
-    }
+        /**
+         * Gets the value of the title property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getTitle() {
+            return title;
+        }
 
-    /**
-     * Gets the value of the consortium property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getConsortium()
-    {
-      return consortium;
-    }
+        /**
+         * Sets the value of the title property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setTitle(String value) {
+            this.title = value;
+        }
 
-    /**
-     * Sets the value of the consortium property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setConsortium(String value)
-    {
-      this.consortium = value;
-    }
+        /**
+         * Gets the value of the author property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the author property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getAuthor().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link String }
+         * 
+         * 
+         */
+        public List<String> getAuthor() {
+            if (author == null) {
+                author = new ArrayList<String>();
+            }
+            return this.author;
+        }
 
-    /**
-     * Gets the value of the submissionDate property.
-     * 
-     * @return possible object is {@link XMLGregorianCalendar }
-     * 
-     */
-    public XMLGregorianCalendar getSubmissionDate()
-    {
-      return submissionDate;
-    }
+        /**
+         * Gets the value of the applicant property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the applicant property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getApplicant().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link String }
+         * 
+         * 
+         */
+        public List<String> getApplicant() {
+            if (applicant == null) {
+                applicant = new ArrayList<String>();
+            }
+            return this.applicant;
+        }
 
-    /**
-     * Sets the value of the submissionDate property.
-     * 
-     * @param value
-     *          allowed object is {@link XMLGregorianCalendar }
-     * 
-     */
-    public void setSubmissionDate(XMLGregorianCalendar value)
-    {
-      this.submissionDate = value;
-    }
+        /**
+         * Gets the value of the consortium property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getConsortium() {
+            return consortium;
+        }
 
-    /**
-     * Gets the value of the journal property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getJournal()
-    {
-      return journal;
-    }
+        /**
+         * Sets the value of the consortium property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setConsortium(String value) {
+            this.consortium = value;
+        }
 
-    /**
-     * Sets the value of the journal property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setJournal(String value)
-    {
-      this.journal = value;
-    }
+        /**
+         * Gets the value of the submissionDate property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link XMLGregorianCalendar }
+         *     
+         */
+        public XMLGregorianCalendar getSubmissionDate() {
+            return submissionDate;
+        }
 
-    /**
-     * Gets the value of the year property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getYear()
-    {
-      return year;
-    }
+        /**
+         * Sets the value of the submissionDate property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link XMLGregorianCalendar }
+         *     
+         */
+        public void setSubmissionDate(XMLGregorianCalendar value) {
+            this.submissionDate = value;
+        }
 
-    /**
-     * Sets the value of the year property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setYear(String value)
-    {
-      this.year = value;
-    }
+        /**
+         * Gets the value of the journal property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getJournal() {
+            return journal;
+        }
 
-    /**
-     * Gets the value of the volume property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getVolume()
-    {
-      return volume;
-    }
+        /**
+         * Sets the value of the journal property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setJournal(String value) {
+            this.journal = value;
+        }
 
-    /**
-     * Sets the value of the volume property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setVolume(String value)
-    {
-      this.volume = value;
-    }
+        /**
+         * Gets the value of the year property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getYear() {
+            return year;
+        }
 
-    /**
-     * Gets the value of the issue property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getIssue()
-    {
-      return issue;
-    }
+        /**
+         * Sets the value of the year property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setYear(String value) {
+            this.year = value;
+        }
 
-    /**
-     * Sets the value of the issue property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setIssue(String value)
-    {
-      this.issue = value;
-    }
+        /**
+         * Gets the value of the volume property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getVolume() {
+            return volume;
+        }
 
-    /**
-     * Gets the value of the firstPage property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getFirstPage()
-    {
-      return firstPage;
-    }
+        /**
+         * Sets the value of the volume property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setVolume(String value) {
+            this.volume = value;
+        }
 
-    /**
-     * Sets the value of the firstPage property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setFirstPage(String value)
-    {
-      this.firstPage = value;
-    }
+        /**
+         * Gets the value of the issue property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getIssue() {
+            return issue;
+        }
 
-    /**
-     * Gets the value of the lastPage property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getLastPage()
-    {
-      return lastPage;
-    }
+        /**
+         * Sets the value of the issue property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setIssue(String value) {
+            this.issue = value;
+        }
 
-    /**
-     * Sets the value of the lastPage property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setLastPage(String value)
-    {
-      this.lastPage = value;
-    }
+        /**
+         * Gets the value of the firstPage property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getFirstPage() {
+            return firstPage;
+        }
 
-    /**
-     * Gets the value of the comment property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getComment()
-    {
-      return comment;
-    }
+        /**
+         * Sets the value of the firstPage property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setFirstPage(String value) {
+            this.firstPage = value;
+        }
 
-    /**
-     * Sets the value of the comment property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setComment(String value)
-    {
-      this.comment = value;
-    }
+        /**
+         * Gets the value of the lastPage property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getLastPage() {
+            return lastPage;
+        }
 
-    /**
-     * Gets the value of the referenceLocation property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getReferenceLocation()
-    {
-      return referenceLocation;
-    }
+        /**
+         * Sets the value of the lastPage property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setLastPage(String value) {
+            this.lastPage = value;
+        }
 
-    /**
-     * Sets the value of the referenceLocation property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setReferenceLocation(String value)
-    {
-      this.referenceLocation = value;
-    }
+        /**
+         * Gets the value of the comment property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getComment() {
+            return comment;
+        }
 
-    /**
-     * Gets the value of the xref property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the xref property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * 
-     * <pre>
-     * getXref().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list {@link XrefType
-     * }
-     * 
-     * 
-     */
-    public List<XrefType> getXref()
-    {
-      if (xref == null)
-      {
-        xref = new ArrayList<XrefType>();
-      }
-      return this.xref;
-    }
+        /**
+         * Sets the value of the comment property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setComment(String value) {
+            this.comment = value;
+        }
 
-    /**
-     * Gets the value of the type property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getType()
-    {
-      return type;
-    }
+        /**
+         * Gets the value of the referenceLocation property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getReferenceLocation() {
+            return referenceLocation;
+        }
 
-    /**
-     * Sets the value of the type property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setType(String value)
-    {
-      this.type = value;
-    }
+        /**
+         * Sets the value of the referenceLocation property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setReferenceLocation(String value) {
+            this.referenceLocation = value;
+        }
 
-    /**
-     * Gets the value of the number property.
-     * 
-     * @return possible object is {@link BigInteger }
-     * 
-     */
-    public BigInteger getNumber()
-    {
-      return number;
-    }
+        /**
+         * Gets the value of the xref property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the xref property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getXref().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link XrefType }
+         * 
+         * 
+         */
+        public List<XrefType> getXref() {
+            if (xref == null) {
+                xref = new ArrayList<XrefType>();
+            }
+            return this.xref;
+        }
 
-    /**
-     * Sets the value of the number property.
-     * 
-     * @param value
-     *          allowed object is {@link BigInteger }
-     * 
-     */
-    public void setNumber(BigInteger value)
-    {
-      this.number = value;
-    }
+        /**
+         * Gets the value of the type property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getType() {
+            return type;
+        }
 
-    /**
-     * Gets the value of the location property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getLocation()
-    {
-      return location;
-    }
+        /**
+         * Sets the value of the type property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setType(String value) {
+            this.type = value;
+        }
 
-    /**
-     * Sets the value of the location property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setLocation(String value)
-    {
-      this.location = value;
-    }
+        /**
+         * Gets the value of the number property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link BigInteger }
+         *     
+         */
+        public BigInteger getNumber() {
+            return number;
+        }
+
+        /**
+         * Sets the value of the number property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link BigInteger }
+         *     
+         */
+        public void setNumber(BigInteger value) {
+            this.number = value;
+        }
+
+        /**
+         * Gets the value of the location property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getLocation() {
+            return location;
+        }
+
+        /**
+         * Sets the value of the location property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setLocation(String value) {
+            this.location = value;
+        }
 
-  }
+    }
 
 }
diff --git a/src/jalview/xml/binding/embl/ObjectFactory.java b/src/jalview/xml/binding/embl/ObjectFactory.java
index f622bd6..3e9d660 100644
--- a/src/jalview/xml/binding/embl/ObjectFactory.java
+++ b/src/jalview/xml/binding/embl/ObjectFactory.java
@@ -2,170 +2,158 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2018.09.14 at 02:46:00 PM BST 
+// Generated on: 2023.01.31 at 04:07:09 PM GMT 
 //
 
+
 package jalview.xml.binding.embl;
 
 import javax.xml.bind.annotation.XmlRegistry;
 
+
 /**
- * This object contains factory methods for each Java content interface and Java
- * element interface generated in the jalview.xml.binding.embl package.
- * <p>
- * An ObjectFactory allows you to programatically construct new instances of the
- * Java representation for XML content. The Java representation of XML content
- * can consist of schema derived interfaces and classes representing the binding
- * of schema type definitions, element declarations and model groups. Factory
- * methods for each of these are provided in this class.
+ * This object contains factory methods for each 
+ * Java content interface and Java element interface 
+ * generated in the jalview.xml.binding.embl package. 
+ * <p>An ObjectFactory allows you to programatically 
+ * construct new instances of the Java representation 
+ * for XML content. The Java representation of XML 
+ * content can consist of schema derived interfaces 
+ * and classes representing the binding of schema 
+ * type definitions, element declarations and model 
+ * groups.  Factory methods for each of these are 
+ * provided in this class.
  * 
  */
 @XmlRegistry
-public class ObjectFactory
-{
-
-  /**
-   * Create a new ObjectFactory that can be used to create new instances of
-   * schema derived classes for package: jalview.xml.binding.embl
-   * 
-   */
-  public ObjectFactory()
-  {
-  }
-
-  /**
-   * Create an instance of {@link EntryType }
-   * 
-   */
-  public EntryType createEntryType()
-  {
-    return new EntryType();
-  }
-
-  /**
-   * Create an instance of {@link EntryType.Contig }
-   * 
-   */
-  public EntryType.Contig createEntryTypeContig()
-  {
-    return new EntryType.Contig();
-  }
-
-  /**
-   * Create an instance of {@link EntryType.Assembly }
-   * 
-   */
-  public EntryType.Assembly createEntryTypeAssembly()
-  {
-    return new EntryType.Assembly();
-  }
-
-  /**
-   * Create an instance of {@link EntryType.Feature }
-   * 
-   */
-  public EntryType.Feature createEntryTypeFeature()
-  {
-    return new EntryType.Feature();
-  }
-
-  /**
-   * Create an instance of {@link EntryType.Feature.FeatureTaxon }
-   * 
-   */
-  public EntryType.Feature.FeatureTaxon createEntryTypeFeatureFeatureTaxon()
-  {
-    return new EntryType.Feature.FeatureTaxon();
-  }
-
-  /**
-   * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage }
-   * 
-   */
-  public EntryType.Feature.FeatureTaxon.Lineage createEntryTypeFeatureFeatureTaxonLineage()
-  {
-    return new EntryType.Feature.FeatureTaxon.Lineage();
-  }
-
-  /**
-   * Create an instance of {@link ROOT }
-   * 
-   */
-  public ROOT createROOT()
-  {
-    return new ROOT();
-  }
-
-  /**
-   * Create an instance of {@link EntrySetType }
-   * 
-   */
-  public EntrySetType createEntrySetType()
-  {
-    return new EntrySetType();
-  }
-
-  /**
-   * Create an instance of {@link XrefType }
-   * 
-   */
-  public XrefType createXrefType()
-  {
-    return new XrefType();
-  }
-
-  /**
-   * Create an instance of {@link EntryType.Reference }
-   * 
-   */
-  public EntryType.Reference createEntryTypeReference()
-  {
-    return new EntryType.Reference();
-  }
-
-  /**
-   * Create an instance of {@link EntryType.Contig.Range }
-   * 
-   */
-  public EntryType.Contig.Range createEntryTypeContigRange()
-  {
-    return new EntryType.Contig.Range();
-  }
-
-  /**
-   * Create an instance of {@link EntryType.Contig.Gap }
-   * 
-   */
-  public EntryType.Contig.Gap createEntryTypeContigGap()
-  {
-    return new EntryType.Contig.Gap();
-  }
-
-  /**
-   * Create an instance of {@link EntryType.Assembly.Range }
-   * 
-   */
-  public EntryType.Assembly.Range createEntryTypeAssemblyRange()
-  {
-    return new EntryType.Assembly.Range();
-  }
-
-  /**
-   * Create an instance of {@link EntryType.Feature.Qualifier }
-   * 
-   */
-  public EntryType.Feature.Qualifier createEntryTypeFeatureQualifier()
-  {
-    return new EntryType.Feature.Qualifier();
-  }
-
-  /**
-   * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
-   * 
-   */
-  public EntryType.Feature.FeatureTaxon.Lineage.Taxon createEntryTypeFeatureFeatureTaxonLineageTaxon()
-  {
-    return new EntryType.Feature.FeatureTaxon.Lineage.Taxon();
-  }
+public class ObjectFactory {
+
+
+    /**
+     * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.embl
+     * 
+     */
+    public ObjectFactory() {
+    }
+
+    /**
+     * Create an instance of {@link EntryType }
+     * 
+     */
+    public EntryType createEntryType() {
+        return new EntryType();
+    }
+
+    /**
+     * Create an instance of {@link EntryType.Contig }
+     * 
+     */
+    public EntryType.Contig createEntryTypeContig() {
+        return new EntryType.Contig();
+    }
+
+    /**
+     * Create an instance of {@link EntryType.Assembly }
+     * 
+     */
+    public EntryType.Assembly createEntryTypeAssembly() {
+        return new EntryType.Assembly();
+    }
+
+    /**
+     * Create an instance of {@link EntryType.Feature }
+     * 
+     */
+    public EntryType.Feature createEntryTypeFeature() {
+        return new EntryType.Feature();
+    }
+
+    /**
+     * Create an instance of {@link EntryType.Feature.FeatureTaxon }
+     * 
+     */
+    public EntryType.Feature.FeatureTaxon createEntryTypeFeatureFeatureTaxon() {
+        return new EntryType.Feature.FeatureTaxon();
+    }
+
+    /**
+     * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage }
+     * 
+     */
+    public EntryType.Feature.FeatureTaxon.Lineage createEntryTypeFeatureFeatureTaxonLineage() {
+        return new EntryType.Feature.FeatureTaxon.Lineage();
+    }
+
+    /**
+     * Create an instance of {@link ROOT }
+     * 
+     */
+    public ROOT createROOT() {
+        return new ROOT();
+    }
+
+    /**
+     * Create an instance of {@link EntrySetType }
+     * 
+     */
+    public EntrySetType createEntrySetType() {
+        return new EntrySetType();
+    }
+
+    /**
+     * Create an instance of {@link XrefType }
+     * 
+     */
+    public XrefType createXrefType() {
+        return new XrefType();
+    }
+
+    /**
+     * Create an instance of {@link EntryType.Reference }
+     * 
+     */
+    public EntryType.Reference createEntryTypeReference() {
+        return new EntryType.Reference();
+    }
+
+    /**
+     * Create an instance of {@link EntryType.Contig.Range }
+     * 
+     */
+    public EntryType.Contig.Range createEntryTypeContigRange() {
+        return new EntryType.Contig.Range();
+    }
+
+    /**
+     * Create an instance of {@link EntryType.Contig.Gap }
+     * 
+     */
+    public EntryType.Contig.Gap createEntryTypeContigGap() {
+        return new EntryType.Contig.Gap();
+    }
+
+    /**
+     * Create an instance of {@link EntryType.Assembly.Range }
+     * 
+     */
+    public EntryType.Assembly.Range createEntryTypeAssemblyRange() {
+        return new EntryType.Assembly.Range();
+    }
+
+    /**
+     * Create an instance of {@link EntryType.Feature.Qualifier }
+     * 
+     */
+    public EntryType.Feature.Qualifier createEntryTypeFeatureQualifier() {
+        return new EntryType.Feature.Qualifier();
+    }
+
+    /**
+     * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
+     * 
+     */
+    public EntryType.Feature.FeatureTaxon.Lineage.Taxon createEntryTypeFeatureFeatureTaxonLineageTaxon() {
+        return new EntryType.Feature.FeatureTaxon.Lineage.Taxon();
+    }
 
 }
diff --git a/src/jalview/xml/binding/embl/ROOT.java b/src/jalview/xml/binding/embl/ROOT.java
index 6a09d79..6b8b2ea 100644
--- a/src/jalview/xml/binding/embl/ROOT.java
+++ b/src/jalview/xml/binding/embl/ROOT.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2018.09.14 at 02:46:00 PM BST 
+// Generated on: 2023.01.31 at 04:07:09 PM GMT 
 //
 
+
 package jalview.xml.binding.embl;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,13 +13,11 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>
- * Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType>
@@ -36,59 +35,62 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = { "entrySet", "entry" })
+@XmlType(name = "", propOrder = {
+    "entrySet",
+    "entry"
+})
 @XmlRootElement(name = "ROOT")
-public class ROOT
-{
-
-  protected EntrySetType entrySet;
+public class ROOT {
 
-  protected EntryType entry;
+    protected EntrySetType entrySet;
+    protected EntryType entry;
 
-  /**
-   * Gets the value of the entrySet property.
-   * 
-   * @return possible object is {@link EntrySetType }
-   * 
-   */
-  public EntrySetType getEntrySet()
-  {
-    return entrySet;
-  }
+    /**
+     * Gets the value of the entrySet property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link EntrySetType }
+     *     
+     */
+    public EntrySetType getEntrySet() {
+        return entrySet;
+    }
 
-  /**
-   * Sets the value of the entrySet property.
-   * 
-   * @param value
-   *          allowed object is {@link EntrySetType }
-   * 
-   */
-  public void setEntrySet(EntrySetType value)
-  {
-    this.entrySet = value;
-  }
+    /**
+     * Sets the value of the entrySet property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link EntrySetType }
+     *     
+     */
+    public void setEntrySet(EntrySetType value) {
+        this.entrySet = value;
+    }
 
-  /**
-   * Gets the value of the entry property.
-   * 
-   * @return possible object is {@link EntryType }
-   * 
-   */
-  public EntryType getEntry()
-  {
-    return entry;
-  }
+    /**
+     * Gets the value of the entry property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link EntryType }
+     *     
+     */
+    public EntryType getEntry() {
+        return entry;
+    }
 
-  /**
-   * Sets the value of the entry property.
-   * 
-   * @param value
-   *          allowed object is {@link EntryType }
-   * 
-   */
-  public void setEntry(EntryType value)
-  {
-    this.entry = value;
-  }
+    /**
+     * Sets the value of the entry property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link EntryType }
+     *     
+     */
+    public void setEntry(EntryType value) {
+        this.entry = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/embl/XrefType.java b/src/jalview/xml/binding/embl/XrefType.java
index cdfd438..4aa7e5e 100644
--- a/src/jalview/xml/binding/embl/XrefType.java
+++ b/src/jalview/xml/binding/embl/XrefType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2018.09.14 at 02:46:00 PM BST 
+// Generated on: 2023.01.31 at 04:07:09 PM GMT 
 //
 
+
 package jalview.xml.binding.embl;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,15 +13,13 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
  * Database cross-reference.
  * 
- * <p>
- * Java class for XrefType complex type.
+ * <p>Java class for XrefType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="XrefType">
@@ -38,85 +37,85 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "XrefType")
-public class XrefType
-{
-
-  @XmlAttribute(name = "db", required = true)
-  protected String db;
-
-  @XmlAttribute(name = "id", required = true)
-  protected String id;
+public class XrefType {
 
-  @XmlAttribute(name = "secondaryId")
-  protected String secondaryId;
+    @XmlAttribute(name = "db", required = true)
+    protected String db;
+    @XmlAttribute(name = "id", required = true)
+    protected String id;
+    @XmlAttribute(name = "secondaryId")
+    protected String secondaryId;
 
-  /**
-   * Gets the value of the db property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDb()
-  {
-    return db;
-  }
+    /**
+     * Gets the value of the db property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDb() {
+        return db;
+    }
 
-  /**
-   * Sets the value of the db property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDb(String value)
-  {
-    this.db = value;
-  }
+    /**
+     * Sets the value of the db property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDb(String value) {
+        this.db = value;
+    }
 
-  /**
-   * Gets the value of the id property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getId()
-  {
-    return id;
-  }
+    /**
+     * Gets the value of the id property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getId() {
+        return id;
+    }
 
-  /**
-   * Sets the value of the id property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setId(String value)
-  {
-    this.id = value;
-  }
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setId(String value) {
+        this.id = value;
+    }
 
-  /**
-   * Gets the value of the secondaryId property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getSecondaryId()
-  {
-    return secondaryId;
-  }
+    /**
+     * Gets the value of the secondaryId property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getSecondaryId() {
+        return secondaryId;
+    }
 
-  /**
-   * Sets the value of the secondaryId property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setSecondaryId(String value)
-  {
-    this.secondaryId = value;
-  }
+    /**
+     * Sets the value of the secondaryId property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setSecondaryId(String value) {
+        this.secondaryId = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/AlcodonFrame.java b/src/jalview/xml/binding/jalview/AlcodonFrame.java
index 9a2c488..bee5c06 100644
--- a/src/jalview/xml/binding/jalview/AlcodonFrame.java
+++ b/src/jalview/xml/binding/jalview/AlcodonFrame.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.math.BigInteger;
@@ -17,288 +18,309 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * &lt;p&gt;Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
  * 
- * &lt;p&gt;The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
- * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
- * &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="alcodon" maxOccurs="unbounded"
- * minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
- * name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&amp;gt;
- * &amp;lt;attribute name="pos2"
- * type="{http://www.w3.org/2001/XMLSchema}integer" /&amp;gt; &amp;lt;attribute
- * name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
- * name="alcodMap" maxOccurs="unbounded" minOccurs="0"&amp;gt;
- * &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
- * &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&amp;gt;
- * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="dnasq" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
- * &amp;lt;/sequence&amp;gt; &amp;lt;/restriction&amp;gt;
- * &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
+ * <pre>
+ * &lt;complexType>
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="alcodon" maxOccurs="unbounded" minOccurs="0">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ *                 &lt;attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ *                 &lt;attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *         &lt;element name="alcodMap" maxOccurs="unbounded" minOccurs="0">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;sequence>
+ *                   &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
+ *                 &lt;/sequence>
+ *                 &lt;attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *       &lt;/sequence>
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = { "alcodon", "alcodMap" })
+@XmlType(name = "", propOrder = {
+    "alcodon",
+    "alcodMap"
+})
 @XmlRootElement(name = "AlcodonFrame")
-public class AlcodonFrame
-{
-
-  protected List<AlcodonFrame.Alcodon> alcodon;
-
-  protected List<AlcodonFrame.AlcodMap> alcodMap;
+public class AlcodonFrame {
 
-  /**
-   * Gets the value of the alcodon property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the alcodon property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getAlcodon().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link AlcodonFrame.Alcodon }
-   * 
-   * 
-   */
-  public List<AlcodonFrame.Alcodon> getAlcodon()
-  {
-    if (alcodon == null)
-    {
-      alcodon = new ArrayList<AlcodonFrame.Alcodon>();
-    }
-    return this.alcodon;
-  }
-
-  /**
-   * Gets the value of the alcodMap property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the alcodMap property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getAlcodMap().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link AlcodonFrame.AlcodMap }
-   * 
-   * 
-   */
-  public List<AlcodonFrame.AlcodMap> getAlcodMap()
-  {
-    if (alcodMap == null)
-    {
-      alcodMap = new ArrayList<AlcodonFrame.AlcodMap>();
-    }
-    return this.alcodMap;
-  }
-
-  /**
-   * &lt;p&gt;Java class for anonymous complex type.
-   * 
-   * &lt;p&gt;The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-   * &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
-   * &amp;lt;sequence&amp;gt; &amp;lt;element
-   * ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&amp;gt;
-   * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="dnasq" use="required"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-   * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "mapping" })
-  public static class AlcodMap
-  {
-
-    @XmlElement(name = "Mapping", required = true)
-    protected Mapping mapping;
-
-    @XmlAttribute(name = "dnasq", required = true)
-    protected String dnasq;
+    protected List<AlcodonFrame.Alcodon> alcodon;
+    protected List<AlcodonFrame.AlcodMap> alcodMap;
 
     /**
+     * Gets the value of the alcodon property.
      * 
-     * a Mapping entry and an associated protein sequence
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the alcodon property.
      * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getAlcodon().add(newItem);
+     * </pre>
      * 
-     * @return possible object is {@link Mapping }
      * 
-     */
-    public Mapping getMapping()
-    {
-      return mapping;
-    }
-
-    /**
-     * Sets the value of the mapping property.
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link AlcodonFrame.Alcodon }
      * 
-     * @param value
-     *          allowed object is {@link Mapping }
      * 
      */
-    public void setMapping(Mapping value)
-    {
-      this.mapping = value;
+    public List<AlcodonFrame.Alcodon> getAlcodon() {
+        if (alcodon == null) {
+            alcodon = new ArrayList<AlcodonFrame.Alcodon>();
+        }
+        return this.alcodon;
     }
 
     /**
-     * Gets the value of the dnasq property.
+     * Gets the value of the alcodMap property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the alcodMap property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getAlcodMap().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link AlcodonFrame.AlcodMap }
      * 
-     * @return possible object is {@link String }
      * 
      */
-    public String getDnasq()
-    {
-      return dnasq;
+    public List<AlcodonFrame.AlcodMap> getAlcodMap() {
+        if (alcodMap == null) {
+            alcodMap = new ArrayList<AlcodonFrame.AlcodMap>();
+        }
+        return this.alcodMap;
     }
 
+
     /**
-     * Sets the value of the dnasq property.
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
+     *       &lt;/sequence>
+     *       &lt;attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
      * 
-     * @param value
-     *          allowed object is {@link String }
      * 
      */
-    public void setDnasq(String value)
-    {
-      this.dnasq = value;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "mapping"
+    })
+    public static class AlcodMap {
 
-  }
+        @XmlElement(name = "Mapping", required = true)
+        protected Mapping mapping;
+        @XmlAttribute(name = "dnasq", required = true)
+        protected String dnasq;
 
-  /**
-   * 
-   * specifies a series of aligned codons from an associated DNA sequence
-   * alignment that when translated correspond to columns of a peptide
-   * alignment. Element may have either all pos1,2,3 attributes specified, or
-   * none at all (indicating a gapped column with no translated peptide).
-   * 
-   * 
-   * &lt;p&gt;Java class for anonymous complex type.
-   * 
-   * &lt;p&gt;The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-   * &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
-   * name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&amp;gt;
-   * &amp;lt;attribute name="pos2"
-   * type="{http://www.w3.org/2001/XMLSchema}integer" /&amp;gt;
-   * &amp;lt;attribute name="pos3"
-   * type="{http://www.w3.org/2001/XMLSchema}integer" /&amp;gt;
-   * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class Alcodon
-  {
+        /**
+         * 
+         * 										a Mapping entry and an associated protein sequence
+         * 									
+         * 
+         * @return
+         *     possible object is
+         *     {@link Mapping }
+         *     
+         */
+        public Mapping getMapping() {
+            return mapping;
+        }
 
-    @XmlAttribute(name = "pos1")
-    protected BigInteger pos1;
+        /**
+         * Sets the value of the mapping property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Mapping }
+         *     
+         */
+        public void setMapping(Mapping value) {
+            this.mapping = value;
+        }
 
-    @XmlAttribute(name = "pos2")
-    protected BigInteger pos2;
+        /**
+         * Gets the value of the dnasq property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getDnasq() {
+            return dnasq;
+        }
 
-    @XmlAttribute(name = "pos3")
-    protected BigInteger pos3;
+        /**
+         * Sets the value of the dnasq property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setDnasq(String value) {
+            this.dnasq = value;
+        }
 
-    /**
-     * Gets the value of the pos1 property.
-     * 
-     * @return possible object is {@link BigInteger }
-     * 
-     */
-    public BigInteger getPos1()
-    {
-      return pos1;
     }
 
-    /**
-     * Sets the value of the pos1 property.
-     * 
-     * @param value
-     *          allowed object is {@link BigInteger }
-     * 
-     */
-    public void setPos1(BigInteger value)
-    {
-      this.pos1 = value;
-    }
 
     /**
-     * Gets the value of the pos2 property.
      * 
-     * @return possible object is {@link BigInteger }
+     * 								specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment.
+     * 								Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide).
+     * 							
      * 
-     */
-    public BigInteger getPos2()
-    {
-      return pos2;
-    }
-
-    /**
-     * Sets the value of the pos2 property.
+     * <p>Java class for anonymous complex type.
      * 
-     * @param value
-     *          allowed object is {@link BigInteger }
+     * <p>The following schema fragment specifies the expected content contained within this class.
      * 
-     */
-    public void setPos2(BigInteger value)
-    {
-      this.pos2 = value;
-    }
-
-    /**
-     * Gets the value of the pos3 property.
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       &lt;attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       &lt;attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
      * 
-     * @return possible object is {@link BigInteger }
      * 
      */
-    public BigInteger getPos3()
-    {
-      return pos3;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class Alcodon {
 
-    /**
-     * Sets the value of the pos3 property.
-     * 
-     * @param value
-     *          allowed object is {@link BigInteger }
-     * 
-     */
-    public void setPos3(BigInteger value)
-    {
-      this.pos3 = value;
-    }
+        @XmlAttribute(name = "pos1")
+        protected BigInteger pos1;
+        @XmlAttribute(name = "pos2")
+        protected BigInteger pos2;
+        @XmlAttribute(name = "pos3")
+        protected BigInteger pos3;
+
+        /**
+         * Gets the value of the pos1 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link BigInteger }
+         *     
+         */
+        public BigInteger getPos1() {
+            return pos1;
+        }
 
-  }
+        /**
+         * Sets the value of the pos1 property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link BigInteger }
+         *     
+         */
+        public void setPos1(BigInteger value) {
+            this.pos1 = value;
+        }
+
+        /**
+         * Gets the value of the pos2 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link BigInteger }
+         *     
+         */
+        public BigInteger getPos2() {
+            return pos2;
+        }
+
+        /**
+         * Sets the value of the pos2 property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link BigInteger }
+         *     
+         */
+        public void setPos2(BigInteger value) {
+            this.pos2 = value;
+        }
+
+        /**
+         * Gets the value of the pos3 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link BigInteger }
+         *     
+         */
+        public BigInteger getPos3() {
+            return pos3;
+        }
+
+        /**
+         * Sets the value of the pos3 property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link BigInteger }
+         *     
+         */
+        public void setPos3(BigInteger value) {
+            this.pos3 = value;
+        }
+
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/Annotation.java b/src/jalview/xml/binding/jalview/Annotation.java
index 8d66aa3..8c07465 100644
--- a/src/jalview/xml/binding/jalview/Annotation.java
+++ b/src/jalview/xml/binding/jalview/Annotation.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -16,846 +17,841 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * &lt;p&gt;Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
  * 
- * &lt;p&gt;The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
- * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
- * &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}annotationElement"
- * maxOccurs="unbounded" minOccurs="0"/&amp;gt; &amp;lt;element name="label"
- * type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt; &amp;lt;element
- * name="description" type="{http://www.w3.org/2001/XMLSchema}string"
- * minOccurs="0"/&amp;gt; &amp;lt;element name="thresholdLine"
- * minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
- * name="label" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float"
- * /&amp;gt; &amp;lt;attribute name="colour"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
- * name="property" maxOccurs="unbounded" minOccurs="0"&amp;gt;
- * &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
- * &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&amp;gt; &amp;lt;attribute name="value"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
- * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="graph" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt; &amp;lt;attribute
- * name="graphType" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
- * &amp;lt;attribute name="sequenceRef"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
- * name="groupRef" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;attribute name="graphColour"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
- * name="graphGroup" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
- * &amp;lt;attribute name="graphHeight"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
- * name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;attribute name="scoreOnly"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
- * &amp;lt;attribute name="score"
- * type="{http://www.w3.org/2001/XMLSchema}double" /&amp;gt; &amp;lt;attribute
- * name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
- * &amp;lt;attribute name="centreColLabels"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt; &amp;lt;attribute
- * name="scaleColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&amp;gt; &amp;lt;attribute name="showAllColLabels"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt; &amp;lt;attribute
- * name="autoCalculated" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="false" /&amp;gt; &amp;lt;attribute name="belowAlignment"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
- * &amp;lt;attribute name="calcId"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
+ * <pre>
+ * &lt;complexType>
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element ref="{www.vamsas.ac.uk/jalview/version2}annotationElement" maxOccurs="unbounded" minOccurs="0"/>
+ *         &lt;element name="label" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *         &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         &lt;element name="thresholdLine" minOccurs="0">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                 &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *         &lt;element name="property" maxOccurs="unbounded" minOccurs="0">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *       &lt;/sequence>
+ *       &lt;attribute name="graph" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *       &lt;attribute name="graphType" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="groupRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="graphColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       &lt;attribute name="graphGroup" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       &lt;attribute name="graphHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="scoreOnly" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *       &lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}double" />
+ *       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *       &lt;attribute name="centreColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *       &lt;attribute name="scaleColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *       &lt;attribute name="showAllColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *       &lt;attribute name="autoCalculated" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *       &lt;attribute name="belowAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *       &lt;attribute name="calcId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "",
-  propOrder =
-  { "annotationElement", "label", "description", "thresholdLine",
-      "property" })
+@XmlType(name = "", propOrder = {
+    "annotationElement",
+    "label",
+    "description",
+    "thresholdLine",
+    "property"
+})
 @XmlRootElement(name = "Annotation")
-public class Annotation
-{
+public class Annotation {
 
-  protected List<AnnotationElement> annotationElement;
+    protected List<AnnotationElement> annotationElement;
+    @XmlElement(required = true)
+    protected String label;
+    protected String description;
+    protected Annotation.ThresholdLine thresholdLine;
+    protected List<Annotation.Property> property;
+    @XmlAttribute(name = "graph", required = true)
+    protected boolean graph;
+    @XmlAttribute(name = "graphType")
+    protected Integer graphType;
+    @XmlAttribute(name = "sequenceRef")
+    protected String sequenceRef;
+    @XmlAttribute(name = "groupRef")
+    protected String groupRef;
+    @XmlAttribute(name = "graphColour")
+    protected Integer graphColour;
+    @XmlAttribute(name = "graphGroup")
+    protected Integer graphGroup;
+    @XmlAttribute(name = "graphHeight")
+    protected Integer graphHeight;
+    @XmlAttribute(name = "id")
+    protected String id;
+    @XmlAttribute(name = "scoreOnly")
+    protected Boolean scoreOnly;
+    @XmlAttribute(name = "score")
+    protected Double score;
+    @XmlAttribute(name = "visible")
+    protected Boolean visible;
+    @XmlAttribute(name = "centreColLabels")
+    protected Boolean centreColLabels;
+    @XmlAttribute(name = "scaleColLabels")
+    protected Boolean scaleColLabels;
+    @XmlAttribute(name = "showAllColLabels")
+    protected Boolean showAllColLabels;
+    @XmlAttribute(name = "autoCalculated")
+    protected Boolean autoCalculated;
+    @XmlAttribute(name = "belowAlignment")
+    protected Boolean belowAlignment;
+    @XmlAttribute(name = "calcId")
+    protected String calcId;
 
-  @XmlElement(required = true)
-  protected String label;
-
-  protected String description;
-
-  protected Annotation.ThresholdLine thresholdLine;
-
-  protected List<Annotation.Property> property;
-
-  @XmlAttribute(name = "graph", required = true)
-  protected boolean graph;
-
-  @XmlAttribute(name = "graphType")
-  protected Integer graphType;
-
-  @XmlAttribute(name = "sequenceRef")
-  protected String sequenceRef;
-
-  @XmlAttribute(name = "groupRef")
-  protected String groupRef;
-
-  @XmlAttribute(name = "graphColour")
-  protected Integer graphColour;
-
-  @XmlAttribute(name = "graphGroup")
-  protected Integer graphGroup;
-
-  @XmlAttribute(name = "graphHeight")
-  protected Integer graphHeight;
-
-  @XmlAttribute(name = "id")
-  protected String id;
-
-  @XmlAttribute(name = "scoreOnly")
-  protected Boolean scoreOnly;
-
-  @XmlAttribute(name = "score")
-  protected Double score;
-
-  @XmlAttribute(name = "visible")
-  protected Boolean visible;
-
-  @XmlAttribute(name = "centreColLabels")
-  protected Boolean centreColLabels;
-
-  @XmlAttribute(name = "scaleColLabels")
-  protected Boolean scaleColLabels;
-
-  @XmlAttribute(name = "showAllColLabels")
-  protected Boolean showAllColLabels;
-
-  @XmlAttribute(name = "autoCalculated")
-  protected Boolean autoCalculated;
-
-  @XmlAttribute(name = "belowAlignment")
-  protected Boolean belowAlignment;
-
-  @XmlAttribute(name = "calcId")
-  protected String calcId;
-
-  /**
-   * Gets the value of the annotationElement property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the annotationElement property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getAnnotationElement().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link AnnotationElement }
-   * 
-   * 
-   */
-  public List<AnnotationElement> getAnnotationElement()
-  {
-    if (annotationElement == null)
-    {
-      annotationElement = new ArrayList<AnnotationElement>();
-    }
-    return this.annotationElement;
-  }
-
-  /**
-   * Gets the value of the label property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getLabel()
-  {
-    return label;
-  }
-
-  /**
-   * Sets the value of the label property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setLabel(String value)
-  {
-    this.label = value;
-  }
-
-  /**
-   * Gets the value of the description property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDescription()
-  {
-    return description;
-  }
-
-  /**
-   * Sets the value of the description property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDescription(String value)
-  {
-    this.description = value;
-  }
-
-  /**
-   * Gets the value of the thresholdLine property.
-   * 
-   * @return possible object is {@link Annotation.ThresholdLine }
-   * 
-   */
-  public Annotation.ThresholdLine getThresholdLine()
-  {
-    return thresholdLine;
-  }
-
-  /**
-   * Sets the value of the thresholdLine property.
-   * 
-   * @param value
-   *          allowed object is {@link Annotation.ThresholdLine }
-   * 
-   */
-  public void setThresholdLine(Annotation.ThresholdLine value)
-  {
-    this.thresholdLine = value;
-  }
-
-  /**
-   * Gets the value of the property property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the property property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getProperty().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link Annotation.Property }
-   * 
-   * 
-   */
-  public List<Annotation.Property> getProperty()
-  {
-    if (property == null)
-    {
-      property = new ArrayList<Annotation.Property>();
-    }
-    return this.property;
-  }
-
-  /**
-   * Gets the value of the graph property.
-   * 
-   */
-  public boolean isGraph()
-  {
-    return graph;
-  }
-
-  /**
-   * Sets the value of the graph property.
-   * 
-   */
-  public void setGraph(boolean value)
-  {
-    this.graph = value;
-  }
-
-  /**
-   * Gets the value of the graphType property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getGraphType()
-  {
-    return graphType;
-  }
-
-  /**
-   * Sets the value of the graphType property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setGraphType(Integer value)
-  {
-    this.graphType = value;
-  }
-
-  /**
-   * Gets the value of the sequenceRef property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getSequenceRef()
-  {
-    return sequenceRef;
-  }
-
-  /**
-   * Sets the value of the sequenceRef property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setSequenceRef(String value)
-  {
-    this.sequenceRef = value;
-  }
-
-  /**
-   * Gets the value of the groupRef property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getGroupRef()
-  {
-    return groupRef;
-  }
-
-  /**
-   * Sets the value of the groupRef property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setGroupRef(String value)
-  {
-    this.groupRef = value;
-  }
-
-  /**
-   * Gets the value of the graphColour property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getGraphColour()
-  {
-    return graphColour;
-  }
-
-  /**
-   * Sets the value of the graphColour property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setGraphColour(Integer value)
-  {
-    this.graphColour = value;
-  }
-
-  /**
-   * Gets the value of the graphGroup property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getGraphGroup()
-  {
-    return graphGroup;
-  }
-
-  /**
-   * Sets the value of the graphGroup property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setGraphGroup(Integer value)
-  {
-    this.graphGroup = value;
-  }
-
-  /**
-   * Gets the value of the graphHeight property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getGraphHeight()
-  {
-    return graphHeight;
-  }
-
-  /**
-   * Sets the value of the graphHeight property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setGraphHeight(Integer value)
-  {
-    this.graphHeight = value;
-  }
-
-  /**
-   * Gets the value of the id property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getId()
-  {
-    return id;
-  }
-
-  /**
-   * Sets the value of the id property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setId(String value)
-  {
-    this.id = value;
-  }
-
-  /**
-   * Gets the value of the scoreOnly property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public boolean isScoreOnly()
-  {
-    if (scoreOnly == null)
-    {
-      return false;
-    }
-    else
-    {
-      return scoreOnly;
-    }
-  }
-
-  /**
-   * Sets the value of the scoreOnly property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setScoreOnly(Boolean value)
-  {
-    this.scoreOnly = value;
-  }
-
-  /**
-   * Gets the value of the score property.
-   * 
-   * @return possible object is {@link Double }
-   * 
-   */
-  public Double getScore()
-  {
-    return score;
-  }
-
-  /**
-   * Sets the value of the score property.
-   * 
-   * @param value
-   *          allowed object is {@link Double }
-   * 
-   */
-  public void setScore(Double value)
-  {
-    this.score = value;
-  }
-
-  /**
-   * Gets the value of the visible property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public Boolean isVisible()
-  {
-    return visible;
-  }
-
-  /**
-   * Sets the value of the visible property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setVisible(Boolean value)
-  {
-    this.visible = value;
-  }
-
-  /**
-   * Gets the value of the centreColLabels property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public Boolean isCentreColLabels()
-  {
-    return centreColLabels;
-  }
-
-  /**
-   * Sets the value of the centreColLabels property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setCentreColLabels(Boolean value)
-  {
-    this.centreColLabels = value;
-  }
-
-  /**
-   * Gets the value of the scaleColLabels property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public Boolean isScaleColLabels()
-  {
-    return scaleColLabels;
-  }
-
-  /**
-   * Sets the value of the scaleColLabels property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setScaleColLabels(Boolean value)
-  {
-    this.scaleColLabels = value;
-  }
-
-  /**
-   * Gets the value of the showAllColLabels property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public Boolean isShowAllColLabels()
-  {
-    return showAllColLabels;
-  }
-
-  /**
-   * Sets the value of the showAllColLabels property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setShowAllColLabels(Boolean value)
-  {
-    this.showAllColLabels = value;
-  }
-
-  /**
-   * Gets the value of the autoCalculated property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public boolean isAutoCalculated()
-  {
-    if (autoCalculated == null)
-    {
-      return false;
-    }
-    else
-    {
-      return autoCalculated;
-    }
-  }
-
-  /**
-   * Sets the value of the autoCalculated property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setAutoCalculated(Boolean value)
-  {
-    this.autoCalculated = value;
-  }
-
-  /**
-   * Gets the value of the belowAlignment property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public boolean isBelowAlignment()
-  {
-    if (belowAlignment == null)
-    {
-      return true;
-    }
-    else
-    {
-      return belowAlignment;
-    }
-  }
-
-  /**
-   * Sets the value of the belowAlignment property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setBelowAlignment(Boolean value)
-  {
-    this.belowAlignment = value;
-  }
-
-  /**
-   * Gets the value of the calcId property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getCalcId()
-  {
-    return calcId;
-  }
-
-  /**
-   * Sets the value of the calcId property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setCalcId(String value)
-  {
-    this.calcId = value;
-  }
-
-  /**
-   * &lt;p&gt;Java class for anonymous complex type.
-   * 
-   * &lt;p&gt;The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-   * &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
-   * name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-   * &amp;lt;attribute name="value"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-   * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class Property
-  {
-
-    @XmlAttribute(name = "name")
-    protected String name;
-
-    @XmlAttribute(name = "value")
-    protected String value;
-
-    /**
-     * Gets the value of the name property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getName()
-    {
-      return name;
-    }
-
-    /**
-     * Sets the value of the name property.
+    /**
+     * Gets the value of the annotationElement property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the annotationElement property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getAnnotationElement().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link AnnotationElement }
+     * 
+     * 
+     */
+    public List<AnnotationElement> getAnnotationElement() {
+        if (annotationElement == null) {
+            annotationElement = new ArrayList<AnnotationElement>();
+        }
+        return this.annotationElement;
+    }
+
+    /**
+     * Gets the value of the label property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getLabel() {
+        return label;
+    }
+
+    /**
+     * Sets the value of the label property.
      * 
      * @param value
-     *          allowed object is {@link String }
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setLabel(String value) {
+        this.label = value;
+    }
+
+    /**
+     * Gets the value of the description property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public void setName(String value)
-    {
-      this.name = value;
+    public String getDescription() {
+        return description;
     }
 
     /**
-     * Gets the value of the value property.
+     * Sets the value of the description property.
      * 
-     * @return possible object is {@link String }
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDescription(String value) {
+        this.description = value;
+    }
+
+    /**
+     * Gets the value of the thresholdLine property.
      * 
+     * @return
+     *     possible object is
+     *     {@link Annotation.ThresholdLine }
+     *     
      */
-    public String getValue()
-    {
-      return value;
+    public Annotation.ThresholdLine getThresholdLine() {
+        return thresholdLine;
     }
 
     /**
-     * Sets the value of the value property.
+     * Sets the value of the thresholdLine property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setValue(String value)
-    {
-      this.value = value;
-    }
-
-  }
-
-  /**
-   * &lt;p&gt;Java class for anonymous complex type.
-   * 
-   * &lt;p&gt;The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-   * &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
-   * name="label" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-   * &amp;lt;attribute name="value"
-   * type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt; &amp;lt;attribute
-   * name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
-   * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class ThresholdLine
-  {
-
-    @XmlAttribute(name = "label")
-    protected String label;
+     *     allowed object is
+     *     {@link Annotation.ThresholdLine }
+     *     
+     */
+    public void setThresholdLine(Annotation.ThresholdLine value) {
+        this.thresholdLine = value;
+    }
 
-    @XmlAttribute(name = "value")
-    protected Float value;
+    /**
+     * Gets the value of the property property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the property property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getProperty().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link Annotation.Property }
+     * 
+     * 
+     */
+    public List<Annotation.Property> getProperty() {
+        if (property == null) {
+            property = new ArrayList<Annotation.Property>();
+        }
+        return this.property;
+    }
 
-    @XmlAttribute(name = "colour")
-    protected Integer colour;
+    /**
+     * Gets the value of the graph property.
+     * 
+     */
+    public boolean isGraph() {
+        return graph;
+    }
 
     /**
-     * Gets the value of the label property.
+     * Sets the value of the graph property.
      * 
-     * @return possible object is {@link String }
+     */
+    public void setGraph(boolean value) {
+        this.graph = value;
+    }
+
+    /**
+     * Gets the value of the graphType property.
      * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
      */
-    public String getLabel()
-    {
-      return label;
+    public Integer getGraphType() {
+        return graphType;
     }
 
     /**
-     * Sets the value of the label property.
+     * Sets the value of the graphType property.
      * 
      * @param value
-     *          allowed object is {@link String }
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setGraphType(Integer value) {
+        this.graphType = value;
+    }
+
+    /**
+     * Gets the value of the sequenceRef property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getSequenceRef() {
+        return sequenceRef;
+    }
+
+    /**
+     * Sets the value of the sequenceRef property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setSequenceRef(String value) {
+        this.sequenceRef = value;
+    }
+
+    /**
+     * Gets the value of the groupRef property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getGroupRef() {
+        return groupRef;
+    }
+
+    /**
+     * Sets the value of the groupRef property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setLabel(String value)
-    {
-      this.label = value;
+    public void setGroupRef(String value) {
+        this.groupRef = value;
     }
 
     /**
-     * Gets the value of the value property.
+     * Gets the value of the graphColour property.
      * 
-     * @return possible object is {@link Float }
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
+     */
+    public Integer getGraphColour() {
+        return graphColour;
+    }
+
+    /**
+     * Sets the value of the graphColour property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setGraphColour(Integer value) {
+        this.graphColour = value;
+    }
+
+    /**
+     * Gets the value of the graphGroup property.
      * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
      */
-    public Float getValue()
-    {
-      return value;
+    public Integer getGraphGroup() {
+        return graphGroup;
     }
 
     /**
-     * Sets the value of the value property.
+     * Sets the value of the graphGroup property.
      * 
      * @param value
-     *          allowed object is {@link Float }
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setGraphGroup(Integer value) {
+        this.graphGroup = value;
+    }
+
+    /**
+     * Gets the value of the graphHeight property.
      * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
      */
-    public void setValue(Float value)
-    {
-      this.value = value;
+    public Integer getGraphHeight() {
+        return graphHeight;
     }
 
     /**
-     * Gets the value of the colour property.
+     * Sets the value of the graphHeight property.
      * 
-     * @return possible object is {@link Integer }
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setGraphHeight(Integer value) {
+        this.graphHeight = value;
+    }
+
+    /**
+     * Gets the value of the id property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public Integer getColour()
-    {
-      return colour;
+    public String getId() {
+        return id;
     }
 
     /**
-     * Sets the value of the colour property.
+     * Sets the value of the id property.
      * 
      * @param value
-     *          allowed object is {@link Integer }
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setId(String value) {
+        this.id = value;
+    }
+
+    /**
+     * Gets the value of the scoreOnly property.
      * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
      */
-    public void setColour(Integer value)
-    {
-      this.colour = value;
+    public boolean isScoreOnly() {
+        if (scoreOnly == null) {
+            return false;
+        } else {
+            return scoreOnly;
+        }
     }
 
-  }
+    /**
+     * Sets the value of the scoreOnly property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setScoreOnly(Boolean value) {
+        this.scoreOnly = value;
+    }
+
+    /**
+     * Gets the value of the score property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Double }
+     *     
+     */
+    public Double getScore() {
+        return score;
+    }
+
+    /**
+     * Sets the value of the score property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Double }
+     *     
+     */
+    public void setScore(Double value) {
+        this.score = value;
+    }
+
+    /**
+     * Gets the value of the visible property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public Boolean isVisible() {
+        return visible;
+    }
+
+    /**
+     * Sets the value of the visible property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setVisible(Boolean value) {
+        this.visible = value;
+    }
+
+    /**
+     * Gets the value of the centreColLabels property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public Boolean isCentreColLabels() {
+        return centreColLabels;
+    }
+
+    /**
+     * Sets the value of the centreColLabels property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setCentreColLabels(Boolean value) {
+        this.centreColLabels = value;
+    }
+
+    /**
+     * Gets the value of the scaleColLabels property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public Boolean isScaleColLabels() {
+        return scaleColLabels;
+    }
+
+    /**
+     * Sets the value of the scaleColLabels property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setScaleColLabels(Boolean value) {
+        this.scaleColLabels = value;
+    }
+
+    /**
+     * Gets the value of the showAllColLabels property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public Boolean isShowAllColLabels() {
+        return showAllColLabels;
+    }
+
+    /**
+     * Sets the value of the showAllColLabels property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setShowAllColLabels(Boolean value) {
+        this.showAllColLabels = value;
+    }
+
+    /**
+     * Gets the value of the autoCalculated property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public boolean isAutoCalculated() {
+        if (autoCalculated == null) {
+            return false;
+        } else {
+            return autoCalculated;
+        }
+    }
+
+    /**
+     * Sets the value of the autoCalculated property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setAutoCalculated(Boolean value) {
+        this.autoCalculated = value;
+    }
+
+    /**
+     * Gets the value of the belowAlignment property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public boolean isBelowAlignment() {
+        if (belowAlignment == null) {
+            return true;
+        } else {
+            return belowAlignment;
+        }
+    }
+
+    /**
+     * Sets the value of the belowAlignment property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setBelowAlignment(Boolean value) {
+        this.belowAlignment = value;
+    }
+
+    /**
+     * Gets the value of the calcId property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getCalcId() {
+        return calcId;
+    }
+
+    /**
+     * Sets the value of the calcId property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setCalcId(String value) {
+        this.calcId = value;
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class Property {
+
+        @XmlAttribute(name = "name")
+        protected String name;
+        @XmlAttribute(name = "value")
+        protected String value;
+
+        /**
+         * Gets the value of the name property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getName() {
+            return name;
+        }
+
+        /**
+         * Sets the value of the name property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setName(String value) {
+            this.name = value;
+        }
+
+        /**
+         * Gets the value of the value property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getValue() {
+            return value;
+        }
+
+        /**
+         * Sets the value of the value property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setValue(String value) {
+            this.value = value;
+        }
+
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class ThresholdLine {
+
+        @XmlAttribute(name = "label")
+        protected String label;
+        @XmlAttribute(name = "value")
+        protected Float value;
+        @XmlAttribute(name = "colour")
+        protected Integer colour;
+
+        /**
+         * Gets the value of the label property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getLabel() {
+            return label;
+        }
+
+        /**
+         * Sets the value of the label property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setLabel(String value) {
+            this.label = value;
+        }
+
+        /**
+         * Gets the value of the value property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Float }
+         *     
+         */
+        public Float getValue() {
+            return value;
+        }
+
+        /**
+         * Sets the value of the value property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Float }
+         *     
+         */
+        public void setValue(Float value) {
+            this.value = value;
+        }
+
+        /**
+         * Gets the value of the colour property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getColour() {
+            return colour;
+        }
+
+        /**
+         * Sets the value of the colour property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setColour(Integer value) {
+            this.colour = value;
+        }
+
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
index e697228..522d9c6 100644
--- a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
+++ b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,243 +13,242 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * &lt;p&gt;Java class for AnnotationColourScheme complex type.
+ * <p>Java class for AnnotationColourScheme complex type.
  * 
- * &lt;p&gt;The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
- * &lt;pre&gt; &amp;lt;complexType name="AnnotationColourScheme"&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
- * name="aboveThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
- * &amp;lt;attribute name="annotation"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
- * name="minColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
- * &amp;lt;attribute name="maxColour"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
- * name="colourScheme" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;attribute name="threshold"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt; &amp;lt;attribute
- * name="perSequence" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
- * &amp;lt;attribute name="predefinedColours"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
+ * <pre>
+ * &lt;complexType name="AnnotationColourScheme">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;attribute name="aboveThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       &lt;attribute name="annotation" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="minColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       &lt;attribute name="maxColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       &lt;attribute name="colourScheme" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *       &lt;attribute name="perSequence" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *       &lt;attribute name="predefinedColours" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "AnnotationColourScheme", namespace = "www.jalview.org")
-public class AnnotationColourScheme
-{
-
-  @XmlAttribute(name = "aboveThreshold")
-  protected Integer aboveThreshold;
-
-  @XmlAttribute(name = "annotation")
-  protected String annotation;
-
-  @XmlAttribute(name = "minColour")
-  protected Integer minColour;
-
-  @XmlAttribute(name = "maxColour")
-  protected Integer maxColour;
-
-  @XmlAttribute(name = "colourScheme")
-  protected String colourScheme;
-
-  @XmlAttribute(name = "threshold")
-  protected Float threshold;
-
-  @XmlAttribute(name = "perSequence")
-  protected Boolean perSequence;
-
-  @XmlAttribute(name = "predefinedColours")
-  protected Boolean predefinedColours;
-
-  /**
-   * Gets the value of the aboveThreshold property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getAboveThreshold()
-  {
-    return aboveThreshold;
-  }
-
-  /**
-   * Sets the value of the aboveThreshold property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setAboveThreshold(Integer value)
-  {
-    this.aboveThreshold = value;
-  }
-
-  /**
-   * Gets the value of the annotation property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getAnnotation()
-  {
-    return annotation;
-  }
-
-  /**
-   * Sets the value of the annotation property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setAnnotation(String value)
-  {
-    this.annotation = value;
-  }
-
-  /**
-   * Gets the value of the minColour property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getMinColour()
-  {
-    return minColour;
-  }
-
-  /**
-   * Sets the value of the minColour property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setMinColour(Integer value)
-  {
-    this.minColour = value;
-  }
-
-  /**
-   * Gets the value of the maxColour property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getMaxColour()
-  {
-    return maxColour;
-  }
-
-  /**
-   * Sets the value of the maxColour property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setMaxColour(Integer value)
-  {
-    this.maxColour = value;
-  }
-
-  /**
-   * Gets the value of the colourScheme property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getColourScheme()
-  {
-    return colourScheme;
-  }
-
-  /**
-   * Sets the value of the colourScheme property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setColourScheme(String value)
-  {
-    this.colourScheme = value;
-  }
-
-  /**
-   * Gets the value of the threshold property.
-   * 
-   * @return possible object is {@link Float }
-   * 
-   */
-  public Float getThreshold()
-  {
-    return threshold;
-  }
-
-  /**
-   * Sets the value of the threshold property.
-   * 
-   * @param value
-   *          allowed object is {@link Float }
-   * 
-   */
-  public void setThreshold(Float value)
-  {
-    this.threshold = value;
-  }
-
-  /**
-   * Gets the value of the perSequence property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public Boolean isPerSequence()
-  {
-    return perSequence;
-  }
-
-  /**
-   * Sets the value of the perSequence property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setPerSequence(Boolean value)
-  {
-    this.perSequence = value;
-  }
-
-  /**
-   * Gets the value of the predefinedColours property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public Boolean isPredefinedColours()
-  {
-    return predefinedColours;
-  }
-
-  /**
-   * Sets the value of the predefinedColours property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setPredefinedColours(Boolean value)
-  {
-    this.predefinedColours = value;
-  }
+public class AnnotationColourScheme {
+
+    @XmlAttribute(name = "aboveThreshold")
+    protected Integer aboveThreshold;
+    @XmlAttribute(name = "annotation")
+    protected String annotation;
+    @XmlAttribute(name = "minColour")
+    protected Integer minColour;
+    @XmlAttribute(name = "maxColour")
+    protected Integer maxColour;
+    @XmlAttribute(name = "colourScheme")
+    protected String colourScheme;
+    @XmlAttribute(name = "threshold")
+    protected Float threshold;
+    @XmlAttribute(name = "perSequence")
+    protected Boolean perSequence;
+    @XmlAttribute(name = "predefinedColours")
+    protected Boolean predefinedColours;
+
+    /**
+     * Gets the value of the aboveThreshold property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
+     */
+    public Integer getAboveThreshold() {
+        return aboveThreshold;
+    }
+
+    /**
+     * Sets the value of the aboveThreshold property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setAboveThreshold(Integer value) {
+        this.aboveThreshold = value;
+    }
+
+    /**
+     * Gets the value of the annotation property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getAnnotation() {
+        return annotation;
+    }
+
+    /**
+     * Sets the value of the annotation property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setAnnotation(String value) {
+        this.annotation = value;
+    }
+
+    /**
+     * Gets the value of the minColour property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
+     */
+    public Integer getMinColour() {
+        return minColour;
+    }
+
+    /**
+     * Sets the value of the minColour property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setMinColour(Integer value) {
+        this.minColour = value;
+    }
+
+    /**
+     * Gets the value of the maxColour property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
+     */
+    public Integer getMaxColour() {
+        return maxColour;
+    }
+
+    /**
+     * Sets the value of the maxColour property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setMaxColour(Integer value) {
+        this.maxColour = value;
+    }
+
+    /**
+     * Gets the value of the colourScheme property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getColourScheme() {
+        return colourScheme;
+    }
+
+    /**
+     * Sets the value of the colourScheme property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setColourScheme(String value) {
+        this.colourScheme = value;
+    }
+
+    /**
+     * Gets the value of the threshold property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Float }
+     *     
+     */
+    public Float getThreshold() {
+        return threshold;
+    }
+
+    /**
+     * Sets the value of the threshold property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Float }
+     *     
+     */
+    public void setThreshold(Float value) {
+        this.threshold = value;
+    }
+
+    /**
+     * Gets the value of the perSequence property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public Boolean isPerSequence() {
+        return perSequence;
+    }
+
+    /**
+     * Sets the value of the perSequence property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setPerSequence(Boolean value) {
+        this.perSequence = value;
+    }
+
+    /**
+     * Gets the value of the predefinedColours property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public Boolean isPredefinedColours() {
+        return predefinedColours;
+    }
+
+    /**
+     * Sets the value of the predefinedColours property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setPredefinedColours(Boolean value) {
+        this.predefinedColours = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/AnnotationElement.java b/src/jalview/xml/binding/jalview/AnnotationElement.java
index ec1216b..99d82a7 100644
--- a/src/jalview/xml/binding/jalview/AnnotationElement.java
+++ b/src/jalview/xml/binding/jalview/AnnotationElement.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,186 +14,190 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * &lt;p&gt;Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
  * 
- * &lt;p&gt;The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
- * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
- * &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="displayCharacter"
- * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&amp;gt;
- * &amp;lt;element name="description"
- * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&amp;gt;
- * &amp;lt;element name="secondaryStructure" minOccurs="0"&amp;gt;
- * &amp;lt;simpleType&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}string"&amp;gt; &amp;lt;length
- * value="1"/&amp;gt; &amp;lt;/restriction&amp;gt; &amp;lt;/simpleType&amp;gt;
- * &amp;lt;/element&amp;gt; &amp;lt;element name="value"
- * type="{http://www.w3.org/2001/XMLSchema}float" minOccurs="0"/&amp;gt;
- * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="position" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
- * name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
+ * <pre>
+ * &lt;complexType>
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="displayCharacter" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         &lt;element name="secondaryStructure" minOccurs="0">
+ *           &lt;simpleType>
+ *             &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ *               &lt;length value="1"/>
+ *             &lt;/restriction>
+ *           &lt;/simpleType>
+ *         &lt;/element>
+ *         &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}float" minOccurs="0"/>
+ *       &lt;/sequence>
+ *       &lt;attribute name="position" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "",
-  propOrder =
-  { "displayCharacter", "description", "secondaryStructure", "value" })
+@XmlType(name = "", propOrder = {
+    "displayCharacter",
+    "description",
+    "secondaryStructure",
+    "value"
+})
 @XmlRootElement(name = "annotationElement")
-public class AnnotationElement
-{
-
-  protected String displayCharacter;
-
-  protected String description;
-
-  protected String secondaryStructure;
-
-  protected Float value;
-
-  @XmlAttribute(name = "position", required = true)
-  protected int position;
-
-  @XmlAttribute(name = "colour")
-  protected Integer colour;
-
-  /**
-   * Gets the value of the displayCharacter property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDisplayCharacter()
-  {
-    return displayCharacter;
-  }
-
-  /**
-   * Sets the value of the displayCharacter property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDisplayCharacter(String value)
-  {
-    this.displayCharacter = value;
-  }
-
-  /**
-   * Gets the value of the description property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDescription()
-  {
-    return description;
-  }
-
-  /**
-   * Sets the value of the description property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDescription(String value)
-  {
-    this.description = value;
-  }
-
-  /**
-   * Gets the value of the secondaryStructure property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getSecondaryStructure()
-  {
-    return secondaryStructure;
-  }
-
-  /**
-   * Sets the value of the secondaryStructure property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setSecondaryStructure(String value)
-  {
-    this.secondaryStructure = value;
-  }
-
-  /**
-   * Gets the value of the value property.
-   * 
-   * @return possible object is {@link Float }
-   * 
-   */
-  public Float getValue()
-  {
-    return value;
-  }
-
-  /**
-   * Sets the value of the value property.
-   * 
-   * @param value
-   *          allowed object is {@link Float }
-   * 
-   */
-  public void setValue(Float value)
-  {
-    this.value = value;
-  }
-
-  /**
-   * Gets the value of the position property.
-   * 
-   */
-  public int getPosition()
-  {
-    return position;
-  }
-
-  /**
-   * Sets the value of the position property.
-   * 
-   */
-  public void setPosition(int value)
-  {
-    this.position = value;
-  }
-
-  /**
-   * Gets the value of the colour property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getColour()
-  {
-    return colour;
-  }
-
-  /**
-   * Sets the value of the colour property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setColour(Integer value)
-  {
-    this.colour = value;
-  }
+public class AnnotationElement {
+
+    protected String displayCharacter;
+    protected String description;
+    protected String secondaryStructure;
+    protected Float value;
+    @XmlAttribute(name = "position", required = true)
+    protected int position;
+    @XmlAttribute(name = "colour")
+    protected Integer colour;
+
+    /**
+     * Gets the value of the displayCharacter property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDisplayCharacter() {
+        return displayCharacter;
+    }
+
+    /**
+     * Sets the value of the displayCharacter property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDisplayCharacter(String value) {
+        this.displayCharacter = value;
+    }
+
+    /**
+     * Gets the value of the description property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDescription() {
+        return description;
+    }
+
+    /**
+     * Sets the value of the description property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDescription(String value) {
+        this.description = value;
+    }
+
+    /**
+     * Gets the value of the secondaryStructure property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getSecondaryStructure() {
+        return secondaryStructure;
+    }
+
+    /**
+     * Sets the value of the secondaryStructure property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setSecondaryStructure(String value) {
+        this.secondaryStructure = value;
+    }
+
+    /**
+     * Gets the value of the value property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Float }
+     *     
+     */
+    public Float getValue() {
+        return value;
+    }
+
+    /**
+     * Sets the value of the value property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Float }
+     *     
+     */
+    public void setValue(Float value) {
+        this.value = value;
+    }
+
+    /**
+     * Gets the value of the position property.
+     * 
+     */
+    public int getPosition() {
+        return position;
+    }
+
+    /**
+     * Sets the value of the position property.
+     * 
+     */
+    public void setPosition(int value) {
+        this.position = value;
+    }
+
+    /**
+     * Gets the value of the colour property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
+     */
+    public Integer getColour() {
+        return colour;
+    }
+
+    /**
+     * Sets the value of the colour property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setColour(Integer value) {
+        this.colour = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/DoubleMatrix.java b/src/jalview/xml/binding/jalview/DoubleMatrix.java
index 7ce2892..77c6bb7 100644
--- a/src/jalview/xml/binding/jalview/DoubleMatrix.java
+++ b/src/jalview/xml/binding/jalview/DoubleMatrix.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -15,167 +16,171 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * &lt;p&gt;Java class for DoubleMatrix complex type.
+ * <p>Java class for DoubleMatrix complex type.
  * 
- * &lt;p&gt;The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
- * &lt;pre&gt; &amp;lt;complexType name="DoubleMatrix"&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="row"
- * type="{www.jalview.org}DoubleVector" maxOccurs="unbounded"
- * minOccurs="0"/&amp;gt; &amp;lt;element name="D"
- * type="{www.jalview.org}DoubleVector" minOccurs="0"/&amp;gt; &amp;lt;element
- * name="E" type="{www.jalview.org}DoubleVector" minOccurs="0"/&amp;gt;
- * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="rows"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
- * name="columns" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
+ * <pre>
+ * &lt;complexType name="DoubleMatrix">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="row" type="{www.jalview.org}DoubleVector" maxOccurs="unbounded" minOccurs="0"/>
+ *         &lt;element name="D" type="{www.jalview.org}DoubleVector" minOccurs="0"/>
+ *         &lt;element name="E" type="{www.jalview.org}DoubleVector" minOccurs="0"/>
+ *       &lt;/sequence>
+ *       &lt;attribute name="rows" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       &lt;attribute name="columns" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "DoubleMatrix",
-  namespace = "www.jalview.org",
-  propOrder =
-  { "row", "d", "e" })
-public class DoubleMatrix
-{
-
-  protected List<DoubleVector> row;
-
-  @XmlElement(name = "D")
-  protected DoubleVector d;
-
-  @XmlElement(name = "E")
-  protected DoubleVector e;
-
-  @XmlAttribute(name = "rows")
-  protected Integer rows;
-
-  @XmlAttribute(name = "columns")
-  protected Integer columns;
-
-  /**
-   * Gets the value of the row property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the row property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getRow().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link DoubleVector }
-   * 
-   * 
-   */
-  public List<DoubleVector> getRow()
-  {
-    if (row == null)
-    {
-      row = new ArrayList<DoubleVector>();
+@XmlType(name = "DoubleMatrix", namespace = "www.jalview.org", propOrder = {
+    "row",
+    "d",
+    "e"
+})
+public class DoubleMatrix {
+
+    protected List<DoubleVector> row;
+    @XmlElement(name = "D")
+    protected DoubleVector d;
+    @XmlElement(name = "E")
+    protected DoubleVector e;
+    @XmlAttribute(name = "rows")
+    protected Integer rows;
+    @XmlAttribute(name = "columns")
+    protected Integer columns;
+
+    /**
+     * Gets the value of the row property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the row property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getRow().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link DoubleVector }
+     * 
+     * 
+     */
+    public List<DoubleVector> getRow() {
+        if (row == null) {
+            row = new ArrayList<DoubleVector>();
+        }
+        return this.row;
+    }
+
+    /**
+     * Gets the value of the d property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link DoubleVector }
+     *     
+     */
+    public DoubleVector getD() {
+        return d;
+    }
+
+    /**
+     * Sets the value of the d property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link DoubleVector }
+     *     
+     */
+    public void setD(DoubleVector value) {
+        this.d = value;
+    }
+
+    /**
+     * Gets the value of the e property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link DoubleVector }
+     *     
+     */
+    public DoubleVector getE() {
+        return e;
+    }
+
+    /**
+     * Sets the value of the e property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link DoubleVector }
+     *     
+     */
+    public void setE(DoubleVector value) {
+        this.e = value;
+    }
+
+    /**
+     * Gets the value of the rows property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
+     */
+    public Integer getRows() {
+        return rows;
+    }
+
+    /**
+     * Sets the value of the rows property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setRows(Integer value) {
+        this.rows = value;
+    }
+
+    /**
+     * Gets the value of the columns property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
+     */
+    public Integer getColumns() {
+        return columns;
+    }
+
+    /**
+     * Sets the value of the columns property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setColumns(Integer value) {
+        this.columns = value;
     }
-    return this.row;
-  }
-
-  /**
-   * Gets the value of the d property.
-   * 
-   * @return possible object is {@link DoubleVector }
-   * 
-   */
-  public DoubleVector getD()
-  {
-    return d;
-  }
-
-  /**
-   * Sets the value of the d property.
-   * 
-   * @param value
-   *          allowed object is {@link DoubleVector }
-   * 
-   */
-  public void setD(DoubleVector value)
-  {
-    this.d = value;
-  }
-
-  /**
-   * Gets the value of the e property.
-   * 
-   * @return possible object is {@link DoubleVector }
-   * 
-   */
-  public DoubleVector getE()
-  {
-    return e;
-  }
-
-  /**
-   * Sets the value of the e property.
-   * 
-   * @param value
-   *          allowed object is {@link DoubleVector }
-   * 
-   */
-  public void setE(DoubleVector value)
-  {
-    this.e = value;
-  }
-
-  /**
-   * Gets the value of the rows property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getRows()
-  {
-    return rows;
-  }
-
-  /**
-   * Sets the value of the rows property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setRows(Integer value)
-  {
-    this.rows = value;
-  }
-
-  /**
-   * Gets the value of the columns property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getColumns()
-  {
-    return columns;
-  }
-
-  /**
-   * Sets the value of the columns property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setColumns(Integer value)
-  {
-    this.columns = value;
-  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/DoubleVector.java b/src/jalview/xml/binding/jalview/DoubleVector.java
index 4995dd3..f1dad96 100644
--- a/src/jalview/xml/binding/jalview/DoubleVector.java
+++ b/src/jalview/xml/binding/jalview/DoubleVector.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -14,58 +15,62 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * &lt;p&gt;Java class for DoubleVector complex type.
+ * <p>Java class for DoubleVector complex type.
  * 
- * &lt;p&gt;The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
- * &lt;pre&gt; &amp;lt;complexType name="DoubleVector"&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="v"
- * type="{http://www.w3.org/2001/XMLSchema}double" maxOccurs="unbounded"
- * minOccurs="0"/&amp;gt; &amp;lt;/sequence&amp;gt; &amp;lt;/restriction&amp;gt;
- * &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
+ * <pre>
+ * &lt;complexType name="DoubleVector">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="v" type="{http://www.w3.org/2001/XMLSchema}double" maxOccurs="unbounded" minOccurs="0"/>
+ *       &lt;/sequence>
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "DoubleVector",
-  namespace = "www.jalview.org",
-  propOrder =
-  { "v" })
-public class DoubleVector
-{
+@XmlType(name = "DoubleVector", namespace = "www.jalview.org", propOrder = {
+    "v"
+})
+public class DoubleVector {
 
-  @XmlElement(type = Double.class)
-  protected List<Double> v;
+    @XmlElement(type = Double.class)
+    protected List<Double> v;
 
-  /**
-   * Gets the value of the v property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the v property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getV().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link Double }
-   * 
-   * 
-   */
-  public List<Double> getV()
-  {
-    if (v == null)
-    {
-      v = new ArrayList<Double>();
+    /**
+     * Gets the value of the v property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the v property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getV().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link Double }
+     * 
+     * 
+     */
+    public List<Double> getV() {
+        if (v == null) {
+            v = new ArrayList<Double>();
+        }
+        return this.v;
     }
-    return this.v;
-  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/Feature.java b/src/jalview/xml/binding/jalview/Feature.java
index 4c496e5..dac24c4 100644
--- a/src/jalview/xml/binding/jalview/Feature.java
+++ b/src/jalview/xml/binding/jalview/Feature.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -14,350 +15,349 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * &lt;p&gt;Java class for feature complex type.
+ * <p>Java class for feature complex type.
  * 
- * &lt;p&gt;The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
- * &lt;pre&gt; &amp;lt;complexType name="feature"&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="otherData"
- * maxOccurs="unbounded" minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
- * name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&amp;gt; &amp;lt;attribute name="key2"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
- * name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&amp;gt; &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
- * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="begin" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
- * name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&amp;gt; &amp;lt;attribute name="type" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
- * name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;attribute name="status"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
- * name="featureGroup" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}float"
- * /&amp;gt; &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
+ * <pre>
+ * &lt;complexType name="feature">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="otherData" maxOccurs="unbounded" minOccurs="0">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *       &lt;/sequence>
+ *       &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="status" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="featureGroup" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "feature",
-  namespace = "www.jalview.org",
-  propOrder =
-  { "otherData" })
-public class Feature
-{
-
-  protected List<Feature.OtherData> otherData;
-
-  @XmlAttribute(name = "begin", required = true)
-  protected int begin;
-
-  @XmlAttribute(name = "end", required = true)
-  protected int end;
-
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
-
-  @XmlAttribute(name = "description")
-  protected String description;
-
-  @XmlAttribute(name = "status")
-  protected String status;
-
-  @XmlAttribute(name = "featureGroup")
-  protected String featureGroup;
-
-  @XmlAttribute(name = "score")
-  protected Float score;
-
-  /**
-   * Gets the value of the otherData property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the otherData property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getOtherData().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link Feature.OtherData }
-   * 
-   * 
-   */
-  public List<Feature.OtherData> getOtherData()
-  {
-    if (otherData == null)
-    {
-      otherData = new ArrayList<Feature.OtherData>();
+@XmlType(name = "feature", namespace = "www.jalview.org", propOrder = {
+    "otherData"
+})
+public class Feature {
+
+    protected List<Feature.OtherData> otherData;
+    @XmlAttribute(name = "begin", required = true)
+    protected int begin;
+    @XmlAttribute(name = "end", required = true)
+    protected int end;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
+    @XmlAttribute(name = "description")
+    protected String description;
+    @XmlAttribute(name = "status")
+    protected String status;
+    @XmlAttribute(name = "featureGroup")
+    protected String featureGroup;
+    @XmlAttribute(name = "score")
+    protected Float score;
+
+    /**
+     * Gets the value of the otherData property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the otherData property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getOtherData().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link Feature.OtherData }
+     * 
+     * 
+     */
+    public List<Feature.OtherData> getOtherData() {
+        if (otherData == null) {
+            otherData = new ArrayList<Feature.OtherData>();
+        }
+        return this.otherData;
     }
-    return this.otherData;
-  }
-
-  /**
-   * Gets the value of the begin property.
-   * 
-   */
-  public int getBegin()
-  {
-    return begin;
-  }
-
-  /**
-   * Sets the value of the begin property.
-   * 
-   */
-  public void setBegin(int value)
-  {
-    this.begin = value;
-  }
-
-  /**
-   * Gets the value of the end property.
-   * 
-   */
-  public int getEnd()
-  {
-    return end;
-  }
-
-  /**
-   * Sets the value of the end property.
-   * 
-   */
-  public void setEnd(int value)
-  {
-    this.end = value;
-  }
-
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
-
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
-
-  /**
-   * Gets the value of the description property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDescription()
-  {
-    return description;
-  }
-
-  /**
-   * Sets the value of the description property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDescription(String value)
-  {
-    this.description = value;
-  }
-
-  /**
-   * Gets the value of the status property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getStatus()
-  {
-    return status;
-  }
-
-  /**
-   * Sets the value of the status property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setStatus(String value)
-  {
-    this.status = value;
-  }
-
-  /**
-   * Gets the value of the featureGroup property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getFeatureGroup()
-  {
-    return featureGroup;
-  }
-
-  /**
-   * Sets the value of the featureGroup property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setFeatureGroup(String value)
-  {
-    this.featureGroup = value;
-  }
-
-  /**
-   * Gets the value of the score property.
-   * 
-   * @return possible object is {@link Float }
-   * 
-   */
-  public Float getScore()
-  {
-    return score;
-  }
-
-  /**
-   * Sets the value of the score property.
-   * 
-   * @param value
-   *          allowed object is {@link Float }
-   * 
-   */
-  public void setScore(Float value)
-  {
-    this.score = value;
-  }
-
-  /**
-   * &lt;p&gt;Java class for anonymous complex type.
-   * 
-   * &lt;p&gt;The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-   * &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
-   * name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
-   * /&amp;gt; &amp;lt;attribute name="key2"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
-   * name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
-   * /&amp;gt; &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class OtherData
-  {
-
-    @XmlAttribute(name = "key", required = true)
-    protected String key;
-
-    @XmlAttribute(name = "key2")
-    protected String key2;
-
-    @XmlAttribute(name = "value", required = true)
-    protected String value;
 
     /**
-     * Gets the value of the key property.
+     * Gets the value of the begin property.
      * 
-     * @return possible object is {@link String }
+     */
+    public int getBegin() {
+        return begin;
+    }
+
+    /**
+     * Sets the value of the begin property.
      * 
      */
-    public String getKey()
-    {
-      return key;
+    public void setBegin(int value) {
+        this.begin = value;
     }
 
     /**
-     * Sets the value of the key property.
+     * Gets the value of the end property.
      * 
-     * @param value
-     *          allowed object is {@link String }
+     */
+    public int getEnd() {
+        return end;
+    }
+
+    /**
+     * Sets the value of the end property.
+     * 
+     */
+    public void setEnd(int value) {
+        this.end = value;
+    }
+
+    /**
+     * Gets the value of the type property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public void setKey(String value)
-    {
-      this.key = value;
+    public String getType() {
+        return type;
     }
 
     /**
-     * Gets the value of the key2 property.
+     * Sets the value of the type property.
      * 
-     * @return possible object is {@link String }
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
+
+    /**
+     * Gets the value of the description property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getKey2()
-    {
-      return key2;
+    public String getDescription() {
+        return description;
     }
 
     /**
-     * Sets the value of the key2 property.
+     * Sets the value of the description property.
      * 
      * @param value
-     *          allowed object is {@link String }
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDescription(String value) {
+        this.description = value;
+    }
+
+    /**
+     * Gets the value of the status property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public void setKey2(String value)
-    {
-      this.key2 = value;
+    public String getStatus() {
+        return status;
     }
 
     /**
-     * Gets the value of the value property.
+     * Sets the value of the status property.
      * 
-     * @return possible object is {@link String }
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setStatus(String value) {
+        this.status = value;
+    }
+
+    /**
+     * Gets the value of the featureGroup property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getValue()
-    {
-      return value;
+    public String getFeatureGroup() {
+        return featureGroup;
     }
 
     /**
-     * Sets the value of the value property.
+     * Sets the value of the featureGroup property.
      * 
      * @param value
-     *          allowed object is {@link String }
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setFeatureGroup(String value) {
+        this.featureGroup = value;
+    }
+
+    /**
+     * Gets the value of the score property.
      * 
+     * @return
+     *     possible object is
+     *     {@link Float }
+     *     
      */
-    public void setValue(String value)
-    {
-      this.value = value;
+    public Float getScore() {
+        return score;
     }
 
-  }
+    /**
+     * Sets the value of the score property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Float }
+     *     
+     */
+    public void setScore(Float value) {
+        this.score = value;
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class OtherData {
+
+        @XmlAttribute(name = "key", required = true)
+        protected String key;
+        @XmlAttribute(name = "key2")
+        protected String key2;
+        @XmlAttribute(name = "value", required = true)
+        protected String value;
+
+        /**
+         * Gets the value of the key property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getKey() {
+            return key;
+        }
+
+        /**
+         * Sets the value of the key property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setKey(String value) {
+            this.key = value;
+        }
+
+        /**
+         * Gets the value of the key2 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getKey2() {
+            return key2;
+        }
+
+        /**
+         * Sets the value of the key2 property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setKey2(String value) {
+            this.key2 = value;
+        }
+
+        /**
+         * Gets the value of the value property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getValue() {
+            return value;
+        }
+
+        /**
+         * Sets the value of the value property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setValue(String value) {
+            this.value = value;
+        }
+
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/FeatureMatcher.java b/src/jalview/xml/binding/jalview/FeatureMatcher.java
index 7fd14fa..8a30d89 100644
--- a/src/jalview/xml/binding/jalview/FeatureMatcher.java
+++ b/src/jalview/xml/binding/jalview/FeatureMatcher.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -15,141 +16,145 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * &lt;p&gt;Java class for FeatureMatcher complex type.
+ * <p>Java class for FeatureMatcher complex type.
  * 
- * &lt;p&gt;The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
- * &lt;pre&gt; &amp;lt;complexType name="FeatureMatcher"&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="attributeName"
- * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
- * minOccurs="0"/&amp;gt; &amp;lt;element name="condition"
- * type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt; &amp;lt;element
- * name="value" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
- * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="by"
- * type="{www.jalview.org/colours}FilterBy" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
+ * <pre>
+ * &lt;complexType name="FeatureMatcher">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ *         &lt;element name="condition" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *         &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *       &lt;/sequence>
+ *       &lt;attribute name="by" type="{www.jalview.org/colours}FilterBy" />
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "FeatureMatcher",
-  namespace = "www.jalview.org/colours",
-  propOrder =
-  { "attributeName", "condition", "value" })
-public class FeatureMatcher
-{
-
-  @XmlElement(namespace = "")
-  protected List<String> attributeName;
+@XmlType(name = "FeatureMatcher", namespace = "www.jalview.org/colours", propOrder = {
+    "attributeName",
+    "condition",
+    "value"
+})
+public class FeatureMatcher {
 
-  @XmlElement(namespace = "", required = true)
-  protected String condition;
+    @XmlElement(namespace = "")
+    protected List<String> attributeName;
+    @XmlElement(namespace = "", required = true)
+    protected String condition;
+    @XmlElement(namespace = "", required = true)
+    protected String value;
+    @XmlAttribute(name = "by")
+    protected FilterBy by;
 
-  @XmlElement(namespace = "", required = true)
-  protected String value;
-
-  @XmlAttribute(name = "by")
-  protected FilterBy by;
-
-  /**
-   * Gets the value of the attributeName property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the attributeName property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getAttributeName().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link String }
-   * 
-   * 
-   */
-  public List<String> getAttributeName()
-  {
-    if (attributeName == null)
-    {
-      attributeName = new ArrayList<String>();
+    /**
+     * Gets the value of the attributeName property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the attributeName property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getAttributeName().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
+     * 
+     */
+    public List<String> getAttributeName() {
+        if (attributeName == null) {
+            attributeName = new ArrayList<String>();
+        }
+        return this.attributeName;
     }
-    return this.attributeName;
-  }
 
-  /**
-   * Gets the value of the condition property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getCondition()
-  {
-    return condition;
-  }
+    /**
+     * Gets the value of the condition property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getCondition() {
+        return condition;
+    }
 
-  /**
-   * Sets the value of the condition property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setCondition(String value)
-  {
-    this.condition = value;
-  }
+    /**
+     * Sets the value of the condition property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setCondition(String value) {
+        this.condition = value;
+    }
 
-  /**
-   * Gets the value of the value property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getValue()
-  {
-    return value;
-  }
+    /**
+     * Gets the value of the value property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getValue() {
+        return value;
+    }
 
-  /**
-   * Sets the value of the value property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setValue(String value)
-  {
-    this.value = value;
-  }
+    /**
+     * Sets the value of the value property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setValue(String value) {
+        this.value = value;
+    }
 
-  /**
-   * Gets the value of the by property.
-   * 
-   * @return possible object is {@link FilterBy }
-   * 
-   */
-  public FilterBy getBy()
-  {
-    return by;
-  }
+    /**
+     * Gets the value of the by property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link FilterBy }
+     *     
+     */
+    public FilterBy getBy() {
+        return by;
+    }
 
-  /**
-   * Sets the value of the by property.
-   * 
-   * @param value
-   *          allowed object is {@link FilterBy }
-   * 
-   */
-  public void setBy(FilterBy value)
-  {
-    this.by = value;
-  }
+    /**
+     * Sets the value of the by property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link FilterBy }
+     *     
+     */
+    public void setBy(FilterBy value) {
+        this.by = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
index d2bdaaa..a902a83 100644
--- a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
+++ b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -15,167 +16,177 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
  * A feature match condition, which may be simple or compound
  * 
- * &lt;p&gt;Java class for FeatureMatcherSet complex type.
+ * <p>Java class for FeatureMatcherSet complex type.
  * 
- * &lt;p&gt;The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
- * &lt;pre&gt; &amp;lt;complexType name="FeatureMatcherSet"&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;choice&amp;gt; &amp;lt;element name="matchCondition"
- * type="{www.jalview.org/colours}FeatureMatcher"/&amp;gt; &amp;lt;element
- * name="compoundMatcher"&amp;gt; &amp;lt;complexType&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="matcherSet"
- * type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2"
- * minOccurs="2"/&amp;gt; &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="and"
- * use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;/choice&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
+ * <pre>
+ * &lt;complexType name="FeatureMatcherSet">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;choice>
+ *         &lt;element name="matchCondition" type="{www.jalview.org/colours}FeatureMatcher"/>
+ *         &lt;element name="compoundMatcher">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;sequence>
+ *                   &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
+ *                 &lt;/sequence>
+ *                 &lt;attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *       &lt;/choice>
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "FeatureMatcherSet",
-  namespace = "www.jalview.org/colours",
-  propOrder =
-  { "matchCondition", "compoundMatcher" })
-public class FeatureMatcherSet
-{
-
-  @XmlElement(namespace = "")
-  protected FeatureMatcher matchCondition;
-
-  @XmlElement(namespace = "")
-  protected FeatureMatcherSet.CompoundMatcher compoundMatcher;
-
-  /**
-   * Gets the value of the matchCondition property.
-   * 
-   * @return possible object is {@link FeatureMatcher }
-   * 
-   */
-  public FeatureMatcher getMatchCondition()
-  {
-    return matchCondition;
-  }
-
-  /**
-   * Sets the value of the matchCondition property.
-   * 
-   * @param value
-   *          allowed object is {@link FeatureMatcher }
-   * 
-   */
-  public void setMatchCondition(FeatureMatcher value)
-  {
-    this.matchCondition = value;
-  }
-
-  /**
-   * Gets the value of the compoundMatcher property.
-   * 
-   * @return possible object is {@link FeatureMatcherSet.CompoundMatcher }
-   * 
-   */
-  public FeatureMatcherSet.CompoundMatcher getCompoundMatcher()
-  {
-    return compoundMatcher;
-  }
-
-  /**
-   * Sets the value of the compoundMatcher property.
-   * 
-   * @param value
-   *          allowed object is {@link FeatureMatcherSet.CompoundMatcher }
-   * 
-   */
-  public void setCompoundMatcher(FeatureMatcherSet.CompoundMatcher value)
-  {
-    this.compoundMatcher = value;
-  }
-
-  /**
-   * &lt;p&gt;Java class for anonymous complex type.
-   * 
-   * &lt;p&gt;The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-   * &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
-   * &amp;lt;sequence&amp;gt; &amp;lt;element name="matcherSet"
-   * type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2"
-   * minOccurs="2"/&amp;gt; &amp;lt;/sequence&amp;gt; &amp;lt;attribute
-   * name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean"
-   * /&amp;gt; &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "matcherSet" })
-  public static class CompoundMatcher
-  {
-
-    @XmlElement(namespace = "", required = true)
-    protected List<FeatureMatcherSet> matcherSet;
-
-    @XmlAttribute(name = "and", required = true)
-    protected boolean and;
+@XmlType(name = "FeatureMatcherSet", namespace = "www.jalview.org/colours", propOrder = {
+    "matchCondition",
+    "compoundMatcher"
+})
+public class FeatureMatcherSet {
+
+    @XmlElement(namespace = "")
+    protected FeatureMatcher matchCondition;
+    @XmlElement(namespace = "")
+    protected FeatureMatcherSet.CompoundMatcher compoundMatcher;
 
     /**
-     * Gets the value of the matcherSet property.
-     * 
-     * &lt;p&gt; This accessor method returns a reference to the live list, not
-     * a snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * &lt;CODE&gt;set&lt;/CODE&gt; method for the matcherSet property.
-     * 
-     * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-     * getMatcherSet().add(newItem); &lt;/pre&gt;
-     * 
-     * 
-     * &lt;p&gt; Objects of the following type(s) are allowed in the list
-     * {@link FeatureMatcherSet }
+     * Gets the value of the matchCondition property.
      * 
+     * @return
+     *     possible object is
+     *     {@link FeatureMatcher }
+     *     
+     */
+    public FeatureMatcher getMatchCondition() {
+        return matchCondition;
+    }
+
+    /**
+     * Sets the value of the matchCondition property.
      * 
+     * @param value
+     *     allowed object is
+     *     {@link FeatureMatcher }
+     *     
      */
-    public List<FeatureMatcherSet> getMatcherSet()
-    {
-      if (matcherSet == null)
-      {
-        matcherSet = new ArrayList<FeatureMatcherSet>();
-      }
-      return this.matcherSet;
+    public void setMatchCondition(FeatureMatcher value) {
+        this.matchCondition = value;
     }
 
     /**
-     * Gets the value of the and property.
+     * Gets the value of the compoundMatcher property.
      * 
+     * @return
+     *     possible object is
+     *     {@link FeatureMatcherSet.CompoundMatcher }
+     *     
      */
-    public boolean isAnd()
-    {
-      return and;
+    public FeatureMatcherSet.CompoundMatcher getCompoundMatcher() {
+        return compoundMatcher;
     }
 
     /**
-     * Sets the value of the and property.
+     * Sets the value of the compoundMatcher property.
      * 
+     * @param value
+     *     allowed object is
+     *     {@link FeatureMatcherSet.CompoundMatcher }
+     *     
      */
-    public void setAnd(boolean value)
-    {
-      this.and = value;
+    public void setCompoundMatcher(FeatureMatcherSet.CompoundMatcher value) {
+        this.compoundMatcher = value;
     }
 
-  }
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
+     *       &lt;/sequence>
+     *       &lt;attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "matcherSet"
+    })
+    public static class CompoundMatcher {
+
+        @XmlElement(namespace = "", required = true)
+        protected List<FeatureMatcherSet> matcherSet;
+        @XmlAttribute(name = "and", required = true)
+        protected boolean and;
+
+        /**
+         * Gets the value of the matcherSet property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the matcherSet property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getMatcherSet().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link FeatureMatcherSet }
+         * 
+         * 
+         */
+        public List<FeatureMatcherSet> getMatcherSet() {
+            if (matcherSet == null) {
+                matcherSet = new ArrayList<FeatureMatcherSet>();
+            }
+            return this.matcherSet;
+        }
+
+        /**
+         * Gets the value of the and property.
+         * 
+         */
+        public boolean isAnd() {
+            return and;
+        }
+
+        /**
+         * Sets the value of the and property.
+         * 
+         */
+        public void setAnd(boolean value) {
+            this.and = value;
+        }
+
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/FilterBy.java b/src/jalview/xml/binding/jalview/FilterBy.java
index 9614490..a95d432 100644
--- a/src/jalview/xml/binding/jalview/FilterBy.java
+++ b/src/jalview/xml/binding/jalview/FilterBy.java
@@ -1,60 +1,61 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlEnum;
 import javax.xml.bind.annotation.XmlEnumValue;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * &lt;p&gt;Java class for FilterBy.
+ * <p>Java class for FilterBy.
  * 
- * &lt;p&gt;The following schema fragment specifies the expected content
- * contained within this class. &lt;pre&gt; &amp;lt;simpleType
- * name="FilterBy"&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}string"&amp;gt; &amp;lt;enumeration
- * value="byLabel"/&amp;gt; &amp;lt;enumeration value="byScore"/&amp;gt;
- * &amp;lt;enumeration value="byAttribute"/&amp;gt; &amp;lt;/restriction&amp;gt;
- * &amp;lt;/simpleType&amp;gt; &lt;/pre&gt;
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * <pre>
+ * &lt;simpleType name="FilterBy">
+ *   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ *     &lt;enumeration value="byLabel"/>
+ *     &lt;enumeration value="byScore"/>
+ *     &lt;enumeration value="byAttribute"/>
+ *   &lt;/restriction>
+ * &lt;/simpleType>
+ * </pre>
  * 
  */
 @XmlType(name = "FilterBy", namespace = "www.jalview.org/colours")
 @XmlEnum
-public enum FilterBy
-{
-
-  @XmlEnumValue("byLabel")
-  BY_LABEL("byLabel"), @XmlEnumValue("byScore")
-  BY_SCORE("byScore"), @XmlEnumValue("byAttribute")
-  BY_ATTRIBUTE("byAttribute");
-
-  private final String value;
-
-  FilterBy(String v)
-  {
-    value = v;
-  }
-
-  public String value()
-  {
-    return value;
-  }
-
-  public static FilterBy fromValue(String v)
-  {
-    for (FilterBy c : FilterBy.values())
-    {
-      if (c.value.equals(v))
-      {
-        return c;
-      }
+public enum FilterBy {
+
+    @XmlEnumValue("byLabel")
+    BY_LABEL("byLabel"),
+    @XmlEnumValue("byScore")
+    BY_SCORE("byScore"),
+    @XmlEnumValue("byAttribute")
+    BY_ATTRIBUTE("byAttribute");
+    private final String value;
+
+    FilterBy(String v) {
+        value = v;
+    }
+
+    public String value() {
+        return value;
+    }
+
+    public static FilterBy fromValue(String v) {
+        for (FilterBy c: FilterBy.values()) {
+            if (c.value.equals(v)) {
+                return c;
+            }
+        }
+        throw new IllegalArgumentException(v);
     }
-    throw new IllegalArgumentException(v);
-  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/JalviewModel.java b/src/jalview/xml/binding/jalview/JalviewModel.java
index 9909b08..2de1eba 100644
--- a/src/jalview/xml/binding/jalview/JalviewModel.java
+++ b/src/jalview/xml/binding/jalview/JalviewModel.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -21,6393 +22,6677 @@ import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
 import javax.xml.datatype.XMLGregorianCalendar;
 
+
 /**
- * &lt;p&gt;Java class for JalviewModel complex type.
+ * <p>Java class for JalviewModel complex type.
  * 
- * &lt;p&gt;The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
- * &lt;pre&gt; &amp;lt;complexType name="JalviewModel"&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="creationDate"
- * type="{http://www.w3.org/2001/XMLSchema}dateTime"/&amp;gt; &amp;lt;element
- * name="version" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
- * &amp;lt;element name="vamsasModel"
- * type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="JSeq" maxOccurs="unbounded"
- * minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="features"
- * type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&amp;gt;
- * &amp;lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&amp;gt;
- * &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt; &amp;lt;extension
- * base="{www.jalview.org}pdbentry"&amp;gt; &amp;lt;sequence&amp;gt;
- * &amp;lt;element name="structureState" maxOccurs="unbounded"
- * minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
- * &amp;lt;simpleContent&amp;gt; &amp;lt;extension
- * base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
- * &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
- * &amp;lt;attribute name="visible"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt; &amp;lt;attribute
- * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;attribute name="alignwithAlignPanel"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
- * &amp;lt;attribute name="colourwithAlignPanel"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
- * &amp;lt;attribute name="colourByJmol"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
- * &amp;lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&amp;gt; &amp;lt;/extension&amp;gt; &amp;lt;/simpleContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
- * &amp;lt;/sequence&amp;gt; &amp;lt;/extension&amp;gt;
- * &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt;
- * &amp;lt;/element&amp;gt; &amp;lt;element name="hiddenSequences"
- * type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded"
- * minOccurs="0"/&amp;gt; &amp;lt;element name="rnaViewer" maxOccurs="unbounded"
- * minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="secondaryStructure"
- * maxOccurs="unbounded"&amp;gt; &amp;lt;complexType&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
- * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;attribute name="annotationId" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
- * name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
- * &amp;lt;attribute name="viewerState"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
- * &amp;lt;/sequence&amp;gt; &amp;lt;attGroup
- * ref="{www.jalview.org}swingwindow"/&amp;gt; &amp;lt;attribute name="title"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
- * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;attribute name="dividerLocation"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
- * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
- * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="colour"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
- * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&amp;gt; &amp;lt;attribute name="end" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
- * name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&amp;gt; &amp;lt;attribute name="hidden"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt; &amp;lt;attribute
- * name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&amp;gt; &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
- * name="JGroup" maxOccurs="unbounded" minOccurs="0"&amp;gt;
- * &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
- * &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="seq"
- * type="{http://www.w3.org/2001/XMLSchema}string"
- * maxOccurs="unbounded"/&amp;gt; &amp;lt;element name="annotationColours"
- * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&amp;gt;
- * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="start"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
- * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
- * &amp;lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&amp;gt; &amp;lt;attribute name="colour"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
- * name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
- * &amp;lt;attribute name="pidThreshold"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
- * name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
- * &amp;lt;attribute name="displayBoxes"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt; &amp;lt;attribute
- * name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
- * &amp;lt;attribute name="colourText"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt; &amp;lt;attribute
- * name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
- * &amp;lt;attribute name="textCol2"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
- * name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&amp;gt; &amp;lt;attribute name="showUnconserved"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt; &amp;lt;attribute
- * name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="true" /&amp;gt; &amp;lt;attribute name="showConsensusHistogram"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
- * &amp;lt;attribute name="showSequenceLogo"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
- * &amp;lt;attribute name="normaliseSequenceLogo"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
- * &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&amp;gt; &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
- * name="Viewport" maxOccurs="unbounded" minOccurs="0"&amp;gt;
- * &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
- * &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="AnnotationColours"
- * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&amp;gt;
- * &amp;lt;element name="hiddenColumns" maxOccurs="unbounded"
- * minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
- * name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
- * &amp;lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&amp;gt; &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
- * name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&amp;gt;
- * &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt; &amp;lt;extension
- * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&amp;gt;
- * &amp;lt;attribute name="calcId" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
- * name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="false" /&amp;gt; &amp;lt;attribute name="autoUpdate" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
- * &amp;lt;/extension&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
- * &amp;lt;/sequence&amp;gt; &amp;lt;attGroup
- * ref="{www.jalview.org}swingwindow"/&amp;gt; &amp;lt;attribute
- * name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&amp;gt; &amp;lt;attribute name="pidSelected"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt; &amp;lt;attribute
- * name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;attribute name="consThreshold"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
- * name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
- * &amp;lt;attribute name="title"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
- * name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
- * &amp;lt;attribute name="rightAlignIds"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt; &amp;lt;attribute
- * name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
- * &amp;lt;attribute name="showColourText"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt; &amp;lt;attribute
- * name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="false" /&amp;gt; &amp;lt;attribute name="showBoxes"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt; &amp;lt;attribute
- * name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&amp;gt; &amp;lt;attribute name="renderGaps"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt; &amp;lt;attribute
- * name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&amp;gt; &amp;lt;attribute name="showNPfeatureTooltip"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt; &amp;lt;attribute
- * name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&amp;gt; &amp;lt;attribute name="followHighlight"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
- * &amp;lt;attribute name="followSelection"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
- * &amp;lt;attribute name="showAnnotation"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt; &amp;lt;attribute
- * name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="false" /&amp;gt; &amp;lt;attribute name="showGroupConservation"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
- * &amp;lt;attribute name="showGroupConsensus"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
- * &amp;lt;attribute name="showConsensusHistogram"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
- * &amp;lt;attribute name="showSequenceLogo"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
- * &amp;lt;attribute name="normaliseSequenceLogo"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
- * &amp;lt;attribute name="ignoreGapsinConsensus"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
- * &amp;lt;attribute name="startRes"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
- * name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
- * &amp;lt;attribute name="fontName"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
- * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
- * &amp;lt;attribute name="fontStyle"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
- * name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="true" /&amp;gt; &amp;lt;attribute name="viewName"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
- * name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&amp;gt; &amp;lt;attribute name="gatheredViews"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt; &amp;lt;attribute
- * name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
- * &amp;lt;attribute name="textCol2"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
- * name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&amp;gt; &amp;lt;attribute name="id"
- * type="{http://www.w3.org/2001/XMLSchema}ID" /&amp;gt; &amp;lt;attribute
- * name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;attribute name="showComplementFeatures"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
- * &amp;lt;attribute name="showComplementFeaturesOnTop"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
- * name="UserColours" maxOccurs="unbounded" minOccurs="0"&amp;gt;
- * &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
- * &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="UserColourScheme"
- * type="{www.jalview.org/colours}JalviewUserColours"/&amp;gt;
- * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="id"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
- * name="tree" maxOccurs="unbounded" minOccurs="0"&amp;gt;
- * &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
- * &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence minOccurs="0"&amp;gt; &amp;lt;element name="title"
- * type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt; &amp;lt;element
- * name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
- * &amp;lt;/sequence&amp;gt; &amp;lt;attGroup
- * ref="{www.jalview.org}swingwindow"/&amp;gt; &amp;lt;attribute name="fontName"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
- * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
- * &amp;lt;attribute name="fontStyle"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
- * name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
- * &amp;lt;attribute name="showBootstrap"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt; &amp;lt;attribute
- * name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&amp;gt; &amp;lt;attribute name="markUnlinked"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt; &amp;lt;attribute
- * name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
- * &amp;lt;attribute name="currentTree"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt; &amp;lt;attribute
- * name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&amp;gt;
- * &amp;lt;attribute name="linkToAllViews"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
- * name="PcaViewer" maxOccurs="unbounded" minOccurs="0"&amp;gt;
- * &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
- * &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="sequencePoint"
- * maxOccurs="unbounded"&amp;gt; &amp;lt;complexType&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
- * ref="{www.jalview.org}position"/&amp;gt; &amp;lt;attribute name="sequenceRef"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
- * name="axis" maxOccurs="3" minOccurs="3"&amp;gt; &amp;lt;complexType&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
- * ref="{www.jalview.org}position"/&amp;gt; &amp;lt;/restriction&amp;gt;
- * &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt;
- * &amp;lt;/element&amp;gt; &amp;lt;element name="seqPointMin"&amp;gt;
- * &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
- * &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
- * name="seqPointMax"&amp;gt; &amp;lt;complexType&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
- * ref="{www.jalview.org}position"/&amp;gt; &amp;lt;/restriction&amp;gt;
- * &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt;
- * &amp;lt;/element&amp;gt; &amp;lt;element name="pcaData"
- * type="{www.jalview.org}PcaDataType"/&amp;gt; &amp;lt;/sequence&amp;gt;
- * &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt; &amp;lt;attGroup
- * ref="{www.jalview.org}SimilarityParams"/&amp;gt; &amp;lt;attribute
- * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;attribute name="scoreModelName"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
- * name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
- * &amp;lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&amp;gt; &amp;lt;attribute name="zDim"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
- * name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
- * &amp;lt;attribute name="scaleFactor"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt; &amp;lt;attribute
- * name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
- * &amp;lt;attribute name="linkToAllViews"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
- * name="FeatureSettings" minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="setting" maxOccurs="unbounded"
- * minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="attributeName"
- * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
- * minOccurs="0"/&amp;gt; &amp;lt;element name="matcherSet"
- * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&amp;gt;
- * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="type" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
- * name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&amp;gt; &amp;lt;attribute name="display" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt; &amp;lt;attribute
- * name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
- * &amp;lt;attribute name="mincolour"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
- * name="noValueColour" type="{www.jalview.org/colours}NoValueColour"
- * default="Min" /&amp;gt; &amp;lt;attribute name="threshold"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt; &amp;lt;attribute
- * name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
- * &amp;lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
- * /&amp;gt; &amp;lt;attribute name="min"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt; &amp;lt;attribute
- * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&amp;gt; &amp;lt;attribute name="autoScale"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
- * name="group" maxOccurs="unbounded" minOccurs="0"&amp;gt;
- * &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
- * &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;attribute name="name" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
- * name="display" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
- * &amp;lt;/sequence&amp;gt; &amp;lt;/restriction&amp;gt;
- * &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt;
- * &amp;lt;/element&amp;gt; &amp;lt;/sequence&amp;gt; &amp;lt;/sequence&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
+ * <pre>
+ * &lt;complexType name="JalviewModel">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
+ *         &lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *         &lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
+ *         &lt;sequence>
+ *           &lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0">
+ *             &lt;complexType>
+ *               &lt;complexContent>
+ *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   &lt;sequence>
+ *                     &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+ *                     &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+ *                       &lt;complexType>
+ *                         &lt;complexContent>
+ *                           &lt;extension base="{www.jalview.org}pdbentry">
+ *                             &lt;sequence>
+ *                               &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ *                                 &lt;complexType>
+ *                                   &lt;simpleContent>
+ *                                     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
+ *                                       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+ *                                       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                                       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                                       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                                       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                                       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                     &lt;/extension>
+ *                                   &lt;/simpleContent>
+ *                                 &lt;/complexType>
+ *                               &lt;/element>
+ *                             &lt;/sequence>
+ *                           &lt;/extension>
+ *                         &lt;/complexContent>
+ *                       &lt;/complexType>
+ *                     &lt;/element>
+ *                     &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+ *                     &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+ *                       &lt;complexType>
+ *                         &lt;complexContent>
+ *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             &lt;sequence>
+ *                               &lt;element name="secondaryStructure" maxOccurs="unbounded">
+ *                                 &lt;complexType>
+ *                                   &lt;complexContent>
+ *                                     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                                       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                                       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                     &lt;/restriction>
+ *                                   &lt;/complexContent>
+ *                                 &lt;/complexType>
+ *                               &lt;/element>
+ *                             &lt;/sequence>
+ *                             &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+ *                             &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                           &lt;/restriction>
+ *                         &lt;/complexContent>
+ *                       &lt;/complexType>
+ *                     &lt;/element>
+ *                   &lt;/sequence>
+ *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                 &lt;/restriction>
+ *               &lt;/complexContent>
+ *             &lt;/complexType>
+ *           &lt;/element>
+ *           &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0">
+ *             &lt;complexType>
+ *               &lt;complexContent>
+ *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   &lt;sequence>
+ *                     &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ *                     &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ *                   &lt;/sequence>
+ *                   &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;/restriction>
+ *               &lt;/complexContent>
+ *             &lt;/complexType>
+ *           &lt;/element>
+ *           &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0">
+ *             &lt;complexType>
+ *               &lt;complexContent>
+ *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   &lt;sequence>
+ *                     &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ *                     &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+ *                       &lt;complexType>
+ *                         &lt;complexContent>
+ *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                           &lt;/restriction>
+ *                         &lt;/complexContent>
+ *                       &lt;/complexType>
+ *                     &lt;/element>
+ *                     &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+ *                       &lt;complexType>
+ *                         &lt;complexContent>
+ *                           &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ *                             &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                             &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                           &lt;/extension>
+ *                         &lt;/complexContent>
+ *                       &lt;/complexType>
+ *                     &lt;/element>
+ *                     &lt;element name="overview" minOccurs="0">
+ *                       &lt;complexType>
+ *                         &lt;complexContent>
+ *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+ *                             &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                             &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                           &lt;/restriction>
+ *                         &lt;/complexContent>
+ *                       &lt;/complexType>
+ *                     &lt;/element>
+ *                   &lt;/sequence>
+ *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+ *                   &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ *                   &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                 &lt;/restriction>
+ *               &lt;/complexContent>
+ *             &lt;/complexType>
+ *           &lt;/element>
+ *           &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0">
+ *             &lt;complexType>
+ *               &lt;complexContent>
+ *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   &lt;sequence>
+ *                     &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+ *                   &lt;/sequence>
+ *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;/restriction>
+ *               &lt;/complexContent>
+ *             &lt;/complexType>
+ *           &lt;/element>
+ *           &lt;element name="tree" maxOccurs="unbounded" minOccurs="0">
+ *             &lt;complexType>
+ *               &lt;complexContent>
+ *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   &lt;sequence minOccurs="0">
+ *                     &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *                     &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *                   &lt;/sequence>
+ *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+ *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                   &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ *                   &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                 &lt;/restriction>
+ *               &lt;/complexContent>
+ *             &lt;/complexType>
+ *           &lt;/element>
+ *           &lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
+ *             &lt;complexType>
+ *               &lt;complexContent>
+ *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   &lt;sequence>
+ *                     &lt;element name="sequencePoint" maxOccurs="unbounded">
+ *                       &lt;complexType>
+ *                         &lt;complexContent>
+ *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             &lt;attGroup ref="{www.jalview.org}position"/>
+ *                             &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                           &lt;/restriction>
+ *                         &lt;/complexContent>
+ *                       &lt;/complexType>
+ *                     &lt;/element>
+ *                     &lt;element name="axis" maxOccurs="3" minOccurs="3">
+ *                       &lt;complexType>
+ *                         &lt;complexContent>
+ *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             &lt;attGroup ref="{www.jalview.org}position"/>
+ *                           &lt;/restriction>
+ *                         &lt;/complexContent>
+ *                       &lt;/complexType>
+ *                     &lt;/element>
+ *                     &lt;element name="seqPointMin">
+ *                       &lt;complexType>
+ *                         &lt;complexContent>
+ *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             &lt;attGroup ref="{www.jalview.org}position"/>
+ *                           &lt;/restriction>
+ *                         &lt;/complexContent>
+ *                       &lt;/complexType>
+ *                     &lt;/element>
+ *                     &lt;element name="seqPointMax">
+ *                       &lt;complexType>
+ *                         &lt;complexContent>
+ *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             &lt;attGroup ref="{www.jalview.org}position"/>
+ *                           &lt;/restriction>
+ *                         &lt;/complexContent>
+ *                       &lt;/complexType>
+ *                     &lt;/element>
+ *                     &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
+ *                   &lt;/sequence>
+ *                   &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
+ *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+ *                   &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                   &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                 &lt;/restriction>
+ *               &lt;/complexContent>
+ *             &lt;/complexType>
+ *           &lt;/element>
+ *           &lt;element name="FeatureSettings" minOccurs="0">
+ *             &lt;complexType>
+ *               &lt;complexContent>
+ *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   &lt;sequence>
+ *                     &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
+ *                       &lt;complexType>
+ *                         &lt;complexContent>
+ *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             &lt;sequence>
+ *                               &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ *                               &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ *                             &lt;/sequence>
+ *                             &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                             &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ *                             &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                             &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                           &lt;/restriction>
+ *                         &lt;/complexContent>
+ *                       &lt;/complexType>
+ *                     &lt;/element>
+ *                     &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
+ *                       &lt;complexType>
+ *                         &lt;complexContent>
+ *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                           &lt;/restriction>
+ *                         &lt;/complexContent>
+ *                       &lt;/complexType>
+ *                     &lt;/element>
+ *                   &lt;/sequence>
+ *                 &lt;/restriction>
+ *               &lt;/complexContent>
+ *             &lt;/complexType>
+ *           &lt;/element>
+ *         &lt;/sequence>
+ *       &lt;/sequence>
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "JalviewModel",
-  namespace = "www.jalview.org",
-  propOrder =
-  { "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport",
-      "userColours", "tree", "pcaViewer", "featureSettings" })
-public class JalviewModel
-{
-
-  @XmlElement(required = true)
-  @XmlSchemaType(name = "dateTime")
-  protected XMLGregorianCalendar creationDate;
-
-  @XmlElement(required = true)
-  protected String version;
-
-  @XmlElement(required = true)
-  protected VAMSAS vamsasModel;
-
-  @XmlElement(name = "JSeq")
-  protected List<JalviewModel.JSeq> jSeq;
-
-  @XmlElement(name = "JGroup")
-  protected List<JalviewModel.JGroup> jGroup;
-
-  @XmlElement(name = "Viewport")
-  protected List<JalviewModel.Viewport> viewport;
-
-  @XmlElement(name = "UserColours")
-  protected List<JalviewModel.UserColours> userColours;
-
-  protected List<JalviewModel.Tree> tree;
-
-  @XmlElement(name = "PcaViewer")
-  protected List<JalviewModel.PcaViewer> pcaViewer;
-
-  @XmlElement(name = "FeatureSettings")
-  protected JalviewModel.FeatureSettings featureSettings;
-
-  /**
-   * Gets the value of the creationDate property.
-   * 
-   * @return possible object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public XMLGregorianCalendar getCreationDate()
-  {
-    return creationDate;
-  }
-
-  /**
-   * Sets the value of the creationDate property.
-   * 
-   * @param value
-   *          allowed object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public void setCreationDate(XMLGregorianCalendar value)
-  {
-    this.creationDate = value;
-  }
-
-  /**
-   * Gets the value of the version property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getVersion()
-  {
-    return version;
-  }
-
-  /**
-   * Sets the value of the version property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setVersion(String value)
-  {
-    this.version = value;
-  }
-
-  /**
-   * Gets the value of the vamsasModel property.
-   * 
-   * @return possible object is {@link VAMSAS }
-   * 
-   */
-  public VAMSAS getVamsasModel()
-  {
-    return vamsasModel;
-  }
-
-  /**
-   * Sets the value of the vamsasModel property.
-   * 
-   * @param value
-   *          allowed object is {@link VAMSAS }
-   * 
-   */
-  public void setVamsasModel(VAMSAS value)
-  {
-    this.vamsasModel = value;
-  }
-
-  /**
-   * Gets the value of the jSeq property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the jSeq property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getJSeq().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link JalviewModel.JSeq }
-   * 
-   * 
-   */
-  public List<JalviewModel.JSeq> getJSeq()
-  {
-    if (jSeq == null)
-    {
-      jSeq = new ArrayList<JalviewModel.JSeq>();
-    }
-    return this.jSeq;
-  }
-
-  /**
-   * Gets the value of the jGroup property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the jGroup property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getJGroup().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link JalviewModel.JGroup }
-   * 
-   * 
-   */
-  public List<JalviewModel.JGroup> getJGroup()
-  {
-    if (jGroup == null)
-    {
-      jGroup = new ArrayList<JalviewModel.JGroup>();
-    }
-    return this.jGroup;
-  }
-
-  /**
-   * Gets the value of the viewport property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the viewport property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getViewport().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link JalviewModel.Viewport }
-   * 
-   * 
-   */
-  public List<JalviewModel.Viewport> getViewport()
-  {
-    if (viewport == null)
-    {
-      viewport = new ArrayList<JalviewModel.Viewport>();
-    }
-    return this.viewport;
-  }
-
-  /**
-   * Gets the value of the userColours property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the userColours property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getUserColours().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link JalviewModel.UserColours }
-   * 
-   * 
-   */
-  public List<JalviewModel.UserColours> getUserColours()
-  {
-    if (userColours == null)
-    {
-      userColours = new ArrayList<JalviewModel.UserColours>();
-    }
-    return this.userColours;
-  }
-
-  /**
-   * Gets the value of the tree property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the tree property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getTree().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link JalviewModel.Tree }
-   * 
-   * 
-   */
-  public List<JalviewModel.Tree> getTree()
-  {
-    if (tree == null)
-    {
-      tree = new ArrayList<JalviewModel.Tree>();
-    }
-    return this.tree;
-  }
-
-  /**
-   * Gets the value of the pcaViewer property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the pcaViewer property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getPcaViewer().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link JalviewModel.PcaViewer }
-   * 
-   * 
-   */
-  public List<JalviewModel.PcaViewer> getPcaViewer()
-  {
-    if (pcaViewer == null)
-    {
-      pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
-    }
-    return this.pcaViewer;
-  }
-
-  /**
-   * Gets the value of the featureSettings property.
-   * 
-   * @return possible object is {@link JalviewModel.FeatureSettings }
-   * 
-   */
-  public JalviewModel.FeatureSettings getFeatureSettings()
-  {
-    return featureSettings;
-  }
-
-  /**
-   * Sets the value of the featureSettings property.
-   * 
-   * @param value
-   *          allowed object is {@link JalviewModel.FeatureSettings }
-   * 
-   */
-  public void setFeatureSettings(JalviewModel.FeatureSettings value)
-  {
-    this.featureSettings = value;
-  }
-
-  /**
-   * &lt;p&gt;Java class for anonymous complex type.
-   * 
-   * &lt;p&gt;The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-   * &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
-   * &amp;lt;sequence&amp;gt; &amp;lt;element name="setting"
-   * maxOccurs="unbounded" minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
-   * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
-   * &amp;lt;sequence&amp;gt; &amp;lt;element name="attributeName"
-   * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
-   * minOccurs="0"/&amp;gt; &amp;lt;element name="matcherSet"
-   * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&amp;gt;
-   * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="type" use="required"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
-   * name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
-   * /&amp;gt; &amp;lt;attribute name="display" use="required"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;attribute name="order"
-   * type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt; &amp;lt;attribute
-   * name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
-   * &amp;lt;attribute name="noValueColour"
-   * type="{www.jalview.org/colours}NoValueColour" default="Min" /&amp;gt;
-   * &amp;lt;attribute name="threshold"
-   * type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt; &amp;lt;attribute
-   * name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
-   * &amp;lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
-   * /&amp;gt; &amp;lt;attribute name="min"
-   * type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt; &amp;lt;attribute
-   * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
-   * /&amp;gt; &amp;lt;attribute name="autoScale"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
-   * name="group" maxOccurs="unbounded" minOccurs="0"&amp;gt;
-   * &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-   * &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
-   * name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
-   * /&amp;gt; &amp;lt;attribute name="display" use="required"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
-   * &amp;lt;/sequence&amp;gt; &amp;lt;/restriction&amp;gt;
-   * &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "setting", "group" })
-  public static class FeatureSettings
-  {
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List<JalviewModel.FeatureSettings.Setting> setting;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List<JalviewModel.FeatureSettings.Group> group;
-
-    /**
-     * Gets the value of the setting property.
-     * 
-     * &lt;p&gt; This accessor method returns a reference to the live list, not
-     * a snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * &lt;CODE&gt;set&lt;/CODE&gt; method for the setting property.
-     * 
-     * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-     * getSetting().add(newItem); &lt;/pre&gt;
-     * 
-     * 
-     * &lt;p&gt; Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.FeatureSettings.Setting }
-     * 
-     * 
-     */
-    public List<JalviewModel.FeatureSettings.Setting> getSetting()
-    {
-      if (setting == null)
-      {
-        setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
-      }
-      return this.setting;
-    }
-
-    /**
-     * Gets the value of the group property.
-     * 
-     * &lt;p&gt; This accessor method returns a reference to the live list, not
-     * a snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * &lt;CODE&gt;set&lt;/CODE&gt; method for the group property.
-     * 
-     * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-     * getGroup().add(newItem); &lt;/pre&gt;
-     * 
-     * 
-     * &lt;p&gt; Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.FeatureSettings.Group }
-     * 
-     * 
-     */
-    public List<JalviewModel.FeatureSettings.Group> getGroup()
-    {
-      if (group == null)
-      {
-        group = new ArrayList<JalviewModel.FeatureSettings.Group>();
-      }
-      return this.group;
-    }
-
-    /**
-     * &lt;p&gt;Java class for anonymous complex type.
-     * 
-     * &lt;p&gt;The following schema fragment specifies the expected content
-     * contained within this class.
-     * 
-     * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-     * &amp;lt;restriction
-     * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
-     * &amp;lt;attribute name="name" use="required"
-     * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-     * &amp;lt;attribute name="display" use="required"
-     * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-     * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-     * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class Group
-    {
-
-      @XmlAttribute(name = "name", required = true)
-      protected String name;
-
-      @XmlAttribute(name = "display", required = true)
-      protected boolean display;
-
-      /**
-       * Gets the value of the name property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getName()
-      {
-        return name;
-      }
-
-      /**
-       * Sets the value of the name property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setName(String value)
-      {
-        this.name = value;
-      }
-
-      /**
-       * Gets the value of the display property.
-       * 
-       */
-      public boolean isDisplay()
-      {
-        return display;
-      }
-
-      /**
-       * Sets the value of the display property.
-       * 
-       */
-      public void setDisplay(boolean value)
-      {
-        this.display = value;
-      }
-
-    }
-
-    /**
-     * &lt;p&gt;Java class for anonymous complex type.
-     * 
-     * &lt;p&gt;The following schema fragment specifies the expected content
-     * contained within this class.
-     * 
-     * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-     * &amp;lt;restriction
-     * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
-     * &amp;lt;sequence&amp;gt; &amp;lt;element name="attributeName"
-     * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
-     * minOccurs="0"/&amp;gt; &amp;lt;element name="matcherSet"
-     * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&amp;gt;
-     * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="type" use="required"
-     * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-     * &amp;lt;attribute name="colour" use="required"
-     * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
-     * name="display" use="required"
-     * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-     * &amp;lt;attribute name="order"
-     * type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
-     * &amp;lt;attribute name="mincolour"
-     * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
-     * name="noValueColour" type="{www.jalview.org/colours}NoValueColour"
-     * default="Min" /&amp;gt; &amp;lt;attribute name="threshold"
-     * type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
-     * &amp;lt;attribute name="threshstate"
-     * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
-     * name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
-     * &amp;lt;attribute name="min"
-     * type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
-     * &amp;lt;attribute name="colourByLabel"
-     * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-     * &amp;lt;attribute name="autoScale"
-     * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-     * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-     * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = { "attributeName", "matcherSet" })
-    public static class Setting
-    {
-
-      @XmlElement(namespace = "www.jalview.org")
-      protected List<String> attributeName;
-
-      @XmlElement(namespace = "www.jalview.org")
-      protected FeatureMatcherSet matcherSet;
-
-      @XmlAttribute(name = "type", required = true)
-      protected String type;
-
-      @XmlAttribute(name = "colour", required = true)
-      protected int colour;
-
-      @XmlAttribute(name = "display", required = true)
-      protected boolean display;
-
-      @XmlAttribute(name = "order")
-      protected Float order;
-
-      @XmlAttribute(name = "mincolour")
-      protected Integer mincolour;
-
-      @XmlAttribute(name = "noValueColour")
-      protected NoValueColour noValueColour;
-
-      @XmlAttribute(name = "threshold")
-      protected Float threshold;
-
-      @XmlAttribute(name = "threshstate")
-      protected Integer threshstate;
-
-      @XmlAttribute(name = "max")
-      protected Float max;
-
-      @XmlAttribute(name = "min")
-      protected Float min;
-
-      @XmlAttribute(name = "colourByLabel")
-      protected Boolean colourByLabel;
-
-      @XmlAttribute(name = "autoScale")
-      protected Boolean autoScale;
-
-      /**
-       * Gets the value of the attributeName property.
-       * 
-       * &lt;p&gt; This accessor method returns a reference to the live list,
-       * not a snapshot. Therefore any modification you make to the returned
-       * list will be present inside the JAXB object. This is why there is not a
-       * &lt;CODE&gt;set&lt;/CODE&gt; method for the attributeName property.
-       * 
-       * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-       * getAttributeName().add(newItem); &lt;/pre&gt;
-       * 
-       * 
-       * &lt;p&gt; Objects of the following type(s) are allowed in the list
-       * {@link String }
-       * 
-       * 
-       */
-      public List<String> getAttributeName()
-      {
-        if (attributeName == null)
-        {
-          attributeName = new ArrayList<String>();
-        }
-        return this.attributeName;
-      }
-
-      /**
-       * Gets the value of the matcherSet property.
-       * 
-       * @return possible object is {@link FeatureMatcherSet }
-       * 
-       */
-      public FeatureMatcherSet getMatcherSet()
-      {
-        return matcherSet;
-      }
-
-      /**
-       * Sets the value of the matcherSet property.
-       * 
-       * @param value
-       *          allowed object is {@link FeatureMatcherSet }
-       * 
-       */
-      public void setMatcherSet(FeatureMatcherSet value)
-      {
-        this.matcherSet = value;
-      }
-
-      /**
-       * Gets the value of the type property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getType()
-      {
-        return type;
-      }
-
-      /**
-       * Sets the value of the type property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setType(String value)
-      {
-        this.type = value;
-      }
-
-      /**
-       * Gets the value of the colour property.
-       * 
-       */
-      public int getColour()
-      {
-        return colour;
-      }
-
-      /**
-       * Sets the value of the colour property.
-       * 
-       */
-      public void setColour(int value)
-      {
-        this.colour = value;
-      }
-
-      /**
-       * Gets the value of the display property.
-       * 
-       */
-      public boolean isDisplay()
-      {
-        return display;
-      }
-
-      /**
-       * Sets the value of the display property.
-       * 
-       */
-      public void setDisplay(boolean value)
-      {
-        this.display = value;
-      }
-
-      /**
-       * Gets the value of the order property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getOrder()
-      {
-        return order;
-      }
-
-      /**
-       * Sets the value of the order property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setOrder(Float value)
-      {
-        this.order = value;
-      }
-
-      /**
-       * Gets the value of the mincolour property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getMincolour()
-      {
-        return mincolour;
-      }
-
-      /**
-       * Sets the value of the mincolour property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setMincolour(Integer value)
-      {
-        this.mincolour = value;
-      }
-
-      /**
-       * Gets the value of the noValueColour property.
-       * 
-       * @return possible object is {@link NoValueColour }
-       * 
-       */
-      public NoValueColour getNoValueColour()
-      {
-        if (noValueColour == null)
-        {
-          return NoValueColour.MIN;
-        }
-        else
-        {
-          return noValueColour;
-        }
-      }
-
-      /**
-       * Sets the value of the noValueColour property.
-       * 
-       * @param value
-       *          allowed object is {@link NoValueColour }
-       * 
-       */
-      public void setNoValueColour(NoValueColour value)
-      {
-        this.noValueColour = value;
-      }
-
-      /**
-       * Gets the value of the threshold property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getThreshold()
-      {
-        return threshold;
-      }
-
-      /**
-       * Sets the value of the threshold property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setThreshold(Float value)
-      {
-        this.threshold = value;
-      }
-
-      /**
-       * Gets the value of the threshstate property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getThreshstate()
-      {
-        return threshstate;
-      }
-
-      /**
-       * Sets the value of the threshstate property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setThreshstate(Integer value)
-      {
-        this.threshstate = value;
-      }
-
-      /**
-       * Gets the value of the max property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getMax()
-      {
-        return max;
-      }
-
-      /**
-       * Sets the value of the max property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setMax(Float value)
-      {
-        this.max = value;
-      }
-
-      /**
-       * Gets the value of the min property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getMin()
-      {
-        return min;
-      }
-
-      /**
-       * Sets the value of the min property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setMin(Float value)
-      {
-        this.min = value;
-      }
-
-      /**
-       * Gets the value of the colourByLabel property.
-       * 
-       * @return possible object is {@link Boolean }
-       * 
-       */
-      public Boolean isColourByLabel()
-      {
-        return colourByLabel;
-      }
-
-      /**
-       * Sets the value of the colourByLabel property.
-       * 
-       * @param value
-       *          allowed object is {@link Boolean }
-       * 
-       */
-      public void setColourByLabel(Boolean value)
-      {
-        this.colourByLabel = value;
-      }
-
-      /**
-       * Gets the value of the autoScale property.
-       * 
-       * @return possible object is {@link Boolean }
-       * 
-       */
-      public Boolean isAutoScale()
-      {
-        return autoScale;
-      }
-
-      /**
-       * Sets the value of the autoScale property.
-       * 
-       * @param value
-       *          allowed object is {@link Boolean }
-       * 
-       */
-      public void setAutoScale(Boolean value)
-      {
-        this.autoScale = value;
-      }
-
-    }
-
-  }
-
-  /**
-   * &lt;p&gt;Java class for anonymous complex type.
-   * 
-   * &lt;p&gt;The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-   * &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
-   * &amp;lt;sequence&amp;gt; &amp;lt;element name="seq"
-   * type="{http://www.w3.org/2001/XMLSchema}string"
-   * maxOccurs="unbounded"/&amp;gt; &amp;lt;element name="annotationColours"
-   * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&amp;gt;
-   * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="start"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
-   * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
-   * &amp;lt;attribute name="name"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
-   * name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-   * &amp;lt;attribute name="consThreshold"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
-   * name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
-   * &amp;lt;attribute name="outlineColour"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
-   * name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean"
-   * /&amp;gt; &amp;lt;attribute name="displayText"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;attribute name="colourText"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;attribute name="textCol1"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
-   * name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
-   * &amp;lt;attribute name="textColThreshold"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
-   * name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean"
-   * /&amp;gt; &amp;lt;attribute name="ignoreGapsinConsensus"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
-   * &amp;lt;attribute name="showConsensusHistogram"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
-   * &amp;lt;attribute name="showSequenceLogo"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
-   * &amp;lt;attribute name="normaliseSequenceLogo"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
-   * &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string"
-   * /&amp;gt; &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "seq", "annotationColours" })
-  public static class JGroup
-  {
-
-    @XmlElement(namespace = "www.jalview.org", required = true)
-    protected List<String> seq;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected AnnotationColourScheme annotationColours;
-
-    @XmlAttribute(name = "start")
-    protected Integer start;
-
-    @XmlAttribute(name = "end")
-    protected Integer end;
-
-    @XmlAttribute(name = "name")
-    protected String name;
-
-    @XmlAttribute(name = "colour")
-    protected String colour;
-
-    @XmlAttribute(name = "consThreshold")
-    protected Integer consThreshold;
-
-    @XmlAttribute(name = "pidThreshold")
-    protected Integer pidThreshold;
-
-    @XmlAttribute(name = "outlineColour")
-    protected Integer outlineColour;
-
-    @XmlAttribute(name = "displayBoxes")
-    protected Boolean displayBoxes;
-
-    @XmlAttribute(name = "displayText")
-    protected Boolean displayText;
-
-    @XmlAttribute(name = "colourText")
-    protected Boolean colourText;
-
-    @XmlAttribute(name = "textCol1")
-    protected Integer textCol1;
-
-    @XmlAttribute(name = "textCol2")
-    protected Integer textCol2;
-
-    @XmlAttribute(name = "textColThreshold")
-    protected Integer textColThreshold;
-
-    @XmlAttribute(name = "showUnconserved")
-    protected Boolean showUnconserved;
-
-    @XmlAttribute(name = "ignoreGapsinConsensus")
-    protected Boolean ignoreGapsinConsensus;
-
-    @XmlAttribute(name = "showConsensusHistogram")
-    protected Boolean showConsensusHistogram;
-
-    @XmlAttribute(name = "showSequenceLogo")
-    protected Boolean showSequenceLogo;
-
-    @XmlAttribute(name = "normaliseSequenceLogo")
-    protected Boolean normaliseSequenceLogo;
-
-    @XmlAttribute(name = "id")
-    protected String id;
-
-    /**
-     * Gets the value of the seq property.
-     * 
-     * &lt;p&gt; This accessor method returns a reference to the live list, not
-     * a snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * &lt;CODE&gt;set&lt;/CODE&gt; method for the seq property.
-     * 
-     * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-     * getSeq().add(newItem); &lt;/pre&gt;
-     * 
-     * 
-     * &lt;p&gt; Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
-     * 
-     */
-    public List<String> getSeq()
-    {
-      if (seq == null)
-      {
-        seq = new ArrayList<String>();
-      }
-      return this.seq;
-    }
-
-    /**
-     * Gets the value of the annotationColours property.
-     * 
-     * @return possible object is {@link AnnotationColourScheme }
-     * 
-     */
-    public AnnotationColourScheme getAnnotationColours()
-    {
-      return annotationColours;
-    }
-
-    /**
-     * Sets the value of the annotationColours property.
+@XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
+    "creationDate",
+    "version",
+    "vamsasModel",
+    "jSeq",
+    "jGroup",
+    "viewport",
+    "userColours",
+    "tree",
+    "pcaViewer",
+    "featureSettings"
+})
+public class JalviewModel {
+
+    @XmlElement(required = true)
+    @XmlSchemaType(name = "dateTime")
+    protected XMLGregorianCalendar creationDate;
+    @XmlElement(required = true)
+    protected String version;
+    @XmlElement(required = true)
+    protected VAMSAS vamsasModel;
+    @XmlElement(name = "JSeq")
+    protected List<JalviewModel.JSeq> jSeq;
+    @XmlElement(name = "JGroup")
+    protected List<JalviewModel.JGroup> jGroup;
+    @XmlElement(name = "Viewport")
+    protected List<JalviewModel.Viewport> viewport;
+    @XmlElement(name = "UserColours")
+    protected List<JalviewModel.UserColours> userColours;
+    protected List<JalviewModel.Tree> tree;
+    @XmlElement(name = "PcaViewer")
+    protected List<JalviewModel.PcaViewer> pcaViewer;
+    @XmlElement(name = "FeatureSettings")
+    protected JalviewModel.FeatureSettings featureSettings;
+
+    /**
+     * Gets the value of the creationDate property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link XMLGregorianCalendar }
+     *     
+     */
+    public XMLGregorianCalendar getCreationDate() {
+        return creationDate;
+    }
+
+    /**
+     * Sets the value of the creationDate property.
      * 
      * @param value
-     *          allowed object is {@link AnnotationColourScheme }
-     * 
+     *     allowed object is
+     *     {@link XMLGregorianCalendar }
+     *     
      */
-    public void setAnnotationColours(AnnotationColourScheme value)
-    {
-      this.annotationColours = value;
+    public void setCreationDate(XMLGregorianCalendar value) {
+        this.creationDate = value;
     }
 
     /**
-     * Gets the value of the start property.
-     * 
-     * @return possible object is {@link Integer }
+     * Gets the value of the version property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public Integer getStart()
-    {
-      return start;
+    public String getVersion() {
+        return version;
     }
 
     /**
-     * Sets the value of the start property.
+     * Sets the value of the version property.
      * 
      * @param value
-     *          allowed object is {@link Integer }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setStart(Integer value)
-    {
-      this.start = value;
+    public void setVersion(String value) {
+        this.version = value;
     }
 
     /**
-     * Gets the value of the end property.
-     * 
-     * @return possible object is {@link Integer }
+     * Gets the value of the vamsasModel property.
      * 
+     * @return
+     *     possible object is
+     *     {@link VAMSAS }
+     *     
      */
-    public Integer getEnd()
-    {
-      return end;
+    public VAMSAS getVamsasModel() {
+        return vamsasModel;
     }
 
     /**
-     * Sets the value of the end property.
+     * Sets the value of the vamsasModel property.
      * 
      * @param value
-     *          allowed object is {@link Integer }
-     * 
+     *     allowed object is
+     *     {@link VAMSAS }
+     *     
      */
-    public void setEnd(Integer value)
-    {
-      this.end = value;
+    public void setVamsasModel(VAMSAS value) {
+        this.vamsasModel = value;
     }
 
     /**
-     * Gets the value of the name property.
+     * Gets the value of the jSeq property.
      * 
-     * @return possible object is {@link String }
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the jSeq property.
      * 
-     */
-    public String getName()
-    {
-      return name;
-    }
-
-    /**
-     * Sets the value of the name property.
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getJSeq().add(newItem);
+     * </pre>
      * 
-     * @param value
-     *          allowed object is {@link String }
      * 
-     */
-    public void setName(String value)
-    {
-      this.name = value;
-    }
-
-    /**
-     * Gets the value of the colour property.
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.JSeq }
      * 
-     * @return possible object is {@link String }
      * 
      */
-    public String getColour()
-    {
-      return colour;
+    public List<JalviewModel.JSeq> getJSeq() {
+        if (jSeq == null) {
+            jSeq = new ArrayList<JalviewModel.JSeq>();
+        }
+        return this.jSeq;
     }
 
     /**
-     * Sets the value of the colour property.
+     * Gets the value of the jGroup property.
      * 
-     * @param value
-     *          allowed object is {@link String }
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the jGroup property.
      * 
-     */
-    public void setColour(String value)
-    {
-      this.colour = value;
-    }
-
-    /**
-     * Gets the value of the consThreshold property.
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getJGroup().add(newItem);
+     * </pre>
      * 
-     * @return possible object is {@link Integer }
      * 
-     */
-    public Integer getConsThreshold()
-    {
-      return consThreshold;
-    }
-
-    /**
-     * Sets the value of the consThreshold property.
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.JGroup }
      * 
-     * @param value
-     *          allowed object is {@link Integer }
      * 
      */
-    public void setConsThreshold(Integer value)
-    {
-      this.consThreshold = value;
+    public List<JalviewModel.JGroup> getJGroup() {
+        if (jGroup == null) {
+            jGroup = new ArrayList<JalviewModel.JGroup>();
+        }
+        return this.jGroup;
     }
 
     /**
-     * Gets the value of the pidThreshold property.
+     * Gets the value of the viewport property.
      * 
-     * @return possible object is {@link Integer }
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the viewport property.
      * 
-     */
-    public Integer getPidThreshold()
-    {
-      return pidThreshold;
-    }
-
-    /**
-     * Sets the value of the pidThreshold property.
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getViewport().add(newItem);
+     * </pre>
      * 
-     * @param value
-     *          allowed object is {@link Integer }
      * 
-     */
-    public void setPidThreshold(Integer value)
-    {
-      this.pidThreshold = value;
-    }
-
-    /**
-     * Gets the value of the outlineColour property.
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.Viewport }
      * 
-     * @return possible object is {@link Integer }
      * 
      */
-    public Integer getOutlineColour()
-    {
-      return outlineColour;
+    public List<JalviewModel.Viewport> getViewport() {
+        if (viewport == null) {
+            viewport = new ArrayList<JalviewModel.Viewport>();
+        }
+        return this.viewport;
     }
 
     /**
-     * Sets the value of the outlineColour property.
+     * Gets the value of the userColours property.
      * 
-     * @param value
-     *          allowed object is {@link Integer }
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the userColours property.
      * 
-     */
-    public void setOutlineColour(Integer value)
-    {
-      this.outlineColour = value;
-    }
-
-    /**
-     * Gets the value of the displayBoxes property.
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getUserColours().add(newItem);
+     * </pre>
      * 
-     * @return possible object is {@link Boolean }
      * 
-     */
-    public Boolean isDisplayBoxes()
-    {
-      return displayBoxes;
-    }
-
-    /**
-     * Sets the value of the displayBoxes property.
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.UserColours }
      * 
-     * @param value
-     *          allowed object is {@link Boolean }
      * 
      */
-    public void setDisplayBoxes(Boolean value)
-    {
-      this.displayBoxes = value;
+    public List<JalviewModel.UserColours> getUserColours() {
+        if (userColours == null) {
+            userColours = new ArrayList<JalviewModel.UserColours>();
+        }
+        return this.userColours;
     }
 
     /**
-     * Gets the value of the displayText property.
+     * Gets the value of the tree property.
      * 
-     * @return possible object is {@link Boolean }
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the tree property.
      * 
-     */
-    public Boolean isDisplayText()
-    {
-      return displayText;
-    }
-
-    /**
-     * Sets the value of the displayText property.
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getTree().add(newItem);
+     * </pre>
      * 
-     * @param value
-     *          allowed object is {@link Boolean }
      * 
-     */
-    public void setDisplayText(Boolean value)
-    {
-      this.displayText = value;
-    }
-
-    /**
-     * Gets the value of the colourText property.
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.Tree }
      * 
-     * @return possible object is {@link Boolean }
      * 
      */
-    public Boolean isColourText()
-    {
-      return colourText;
+    public List<JalviewModel.Tree> getTree() {
+        if (tree == null) {
+            tree = new ArrayList<JalviewModel.Tree>();
+        }
+        return this.tree;
     }
 
     /**
-     * Sets the value of the colourText property.
+     * Gets the value of the pcaViewer property.
      * 
-     * @param value
-     *          allowed object is {@link Boolean }
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
      * 
-     */
-    public void setColourText(Boolean value)
-    {
-      this.colourText = value;
-    }
-
-    /**
-     * Gets the value of the textCol1 property.
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getPcaViewer().add(newItem);
+     * </pre>
      * 
-     * @return possible object is {@link Integer }
      * 
-     */
-    public Integer getTextCol1()
-    {
-      return textCol1;
-    }
-
-    /**
-     * Sets the value of the textCol1 property.
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.PcaViewer }
      * 
-     * @param value
-     *          allowed object is {@link Integer }
      * 
      */
-    public void setTextCol1(Integer value)
-    {
-      this.textCol1 = value;
+    public List<JalviewModel.PcaViewer> getPcaViewer() {
+        if (pcaViewer == null) {
+            pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
+        }
+        return this.pcaViewer;
     }
 
     /**
-     * Gets the value of the textCol2 property.
-     * 
-     * @return possible object is {@link Integer }
+     * Gets the value of the featureSettings property.
      * 
+     * @return
+     *     possible object is
+     *     {@link JalviewModel.FeatureSettings }
+     *     
      */
-    public Integer getTextCol2()
-    {
-      return textCol2;
+    public JalviewModel.FeatureSettings getFeatureSettings() {
+        return featureSettings;
     }
 
     /**
-     * Sets the value of the textCol2 property.
+     * Sets the value of the featureSettings property.
      * 
      * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextCol2(Integer value)
-    {
-      this.textCol2 = value;
-    }
-
-    /**
-     * Gets the value of the textColThreshold property.
+     *     allowed object is
+     *     {@link JalviewModel.FeatureSettings }
+     *     
+     */
+    public void setFeatureSettings(JalviewModel.FeatureSettings value) {
+        this.featureSettings = value;
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 &lt;sequence>
+     *                   &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+     *                   &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+     *                 &lt;/sequence>
+     *                 &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+     *                 &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *               &lt;/restriction>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *         &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *               &lt;/restriction>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *       &lt;/sequence>
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
      * 
-     * @return possible object is {@link Integer }
      * 
      */
-    public Integer getTextColThreshold()
-    {
-      return textColThreshold;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "setting",
+        "group"
+    })
+    public static class FeatureSettings {
 
-    /**
-     * Sets the value of the textColThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextColThreshold(Integer value)
-    {
-      this.textColThreshold = value;
-    }
+        @XmlElement(namespace = "www.jalview.org")
+        protected List<JalviewModel.FeatureSettings.Setting> setting;
+        @XmlElement(namespace = "www.jalview.org")
+        protected List<JalviewModel.FeatureSettings.Group> group;
 
-    /**
-     * Gets the value of the showUnconserved property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowUnconserved()
-    {
-      return showUnconserved;
-    }
+        /**
+         * Gets the value of the setting property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the setting property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getSetting().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.FeatureSettings.Setting }
+         * 
+         * 
+         */
+        public List<JalviewModel.FeatureSettings.Setting> getSetting() {
+            if (setting == null) {
+                setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
+            }
+            return this.setting;
+        }
 
-    /**
-     * Sets the value of the showUnconserved property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowUnconserved(Boolean value)
-    {
-      this.showUnconserved = value;
-    }
+        /**
+         * Gets the value of the group property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the group property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getGroup().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.FeatureSettings.Group }
+         * 
+         * 
+         */
+        public List<JalviewModel.FeatureSettings.Group> getGroup() {
+            if (group == null) {
+                group = new ArrayList<JalviewModel.FeatureSettings.Group>();
+            }
+            return this.group;
+        }
 
-    /**
-     * Gets the value of the ignoreGapsinConsensus property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isIgnoreGapsinConsensus()
-    {
-      if (ignoreGapsinConsensus == null)
-      {
-        return true;
-      }
-      else
-      {
-        return ignoreGapsinConsensus;
-      }
-    }
 
-    /**
-     * Sets the value of the ignoreGapsinConsensus property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setIgnoreGapsinConsensus(Boolean value)
-    {
-      this.ignoreGapsinConsensus = value;
-    }
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *     &lt;/restriction>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class Group {
+
+            @XmlAttribute(name = "name", required = true)
+            protected String name;
+            @XmlAttribute(name = "display", required = true)
+            protected boolean display;
+
+            /**
+             * Gets the value of the name property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getName() {
+                return name;
+            }
+
+            /**
+             * Sets the value of the name property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setName(String value) {
+                this.name = value;
+            }
+
+            /**
+             * Gets the value of the display property.
+             * 
+             */
+            public boolean isDisplay() {
+                return display;
+            }
+
+            /**
+             * Sets the value of the display property.
+             * 
+             */
+            public void setDisplay(boolean value) {
+                this.display = value;
+            }
 
-    /**
-     * Gets the value of the showConsensusHistogram property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowConsensusHistogram()
-    {
-      if (showConsensusHistogram == null)
-      {
-        return true;
-      }
-      else
-      {
-        return showConsensusHistogram;
-      }
-    }
+        }
 
-    /**
-     * Sets the value of the showConsensusHistogram property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowConsensusHistogram(Boolean value)
-    {
-      this.showConsensusHistogram = value;
-    }
 
-    /**
-     * Gets the value of the showSequenceLogo property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowSequenceLogo()
-    {
-      if (showSequenceLogo == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showSequenceLogo;
-      }
-    }
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       &lt;sequence>
+         *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+         *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+         *       &lt;/sequence>
+         *       &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *       &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+         *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *       &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *     &lt;/restriction>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "", propOrder = {
+            "attributeName",
+            "matcherSet"
+        })
+        public static class Setting {
+
+            @XmlElement(namespace = "www.jalview.org")
+            protected List<String> attributeName;
+            @XmlElement(namespace = "www.jalview.org")
+            protected FeatureMatcherSet matcherSet;
+            @XmlAttribute(name = "type", required = true)
+            protected String type;
+            @XmlAttribute(name = "colour", required = true)
+            protected int colour;
+            @XmlAttribute(name = "display", required = true)
+            protected boolean display;
+            @XmlAttribute(name = "order")
+            protected Float order;
+            @XmlAttribute(name = "mincolour")
+            protected Integer mincolour;
+            @XmlAttribute(name = "noValueColour")
+            protected NoValueColour noValueColour;
+            @XmlAttribute(name = "threshold")
+            protected Float threshold;
+            @XmlAttribute(name = "threshstate")
+            protected Integer threshstate;
+            @XmlAttribute(name = "max")
+            protected Float max;
+            @XmlAttribute(name = "min")
+            protected Float min;
+            @XmlAttribute(name = "colourByLabel")
+            protected Boolean colourByLabel;
+            @XmlAttribute(name = "autoScale")
+            protected Boolean autoScale;
+
+            /**
+             * Gets the value of the attributeName property.
+             * 
+             * <p>
+             * This accessor method returns a reference to the live list,
+             * not a snapshot. Therefore any modification you make to the
+             * returned list will be present inside the JAXB object.
+             * This is why there is not a <CODE>set</CODE> method for the attributeName property.
+             * 
+             * <p>
+             * For example, to add a new item, do as follows:
+             * <pre>
+             *    getAttributeName().add(newItem);
+             * </pre>
+             * 
+             * 
+             * <p>
+             * Objects of the following type(s) are allowed in the list
+             * {@link String }
+             * 
+             * 
+             */
+            public List<String> getAttributeName() {
+                if (attributeName == null) {
+                    attributeName = new ArrayList<String>();
+                }
+                return this.attributeName;
+            }
+
+            /**
+             * Gets the value of the matcherSet property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link FeatureMatcherSet }
+             *     
+             */
+            public FeatureMatcherSet getMatcherSet() {
+                return matcherSet;
+            }
+
+            /**
+             * Sets the value of the matcherSet property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link FeatureMatcherSet }
+             *     
+             */
+            public void setMatcherSet(FeatureMatcherSet value) {
+                this.matcherSet = value;
+            }
+
+            /**
+             * Gets the value of the type property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getType() {
+                return type;
+            }
+
+            /**
+             * Sets the value of the type property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setType(String value) {
+                this.type = value;
+            }
+
+            /**
+             * Gets the value of the colour property.
+             * 
+             */
+            public int getColour() {
+                return colour;
+            }
+
+            /**
+             * Sets the value of the colour property.
+             * 
+             */
+            public void setColour(int value) {
+                this.colour = value;
+            }
+
+            /**
+             * Gets the value of the display property.
+             * 
+             */
+            public boolean isDisplay() {
+                return display;
+            }
+
+            /**
+             * Sets the value of the display property.
+             * 
+             */
+            public void setDisplay(boolean value) {
+                this.display = value;
+            }
+
+            /**
+             * Gets the value of the order property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getOrder() {
+                return order;
+            }
+
+            /**
+             * Sets the value of the order property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setOrder(Float value) {
+                this.order = value;
+            }
+
+            /**
+             * Gets the value of the mincolour property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getMincolour() {
+                return mincolour;
+            }
+
+            /**
+             * Sets the value of the mincolour property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setMincolour(Integer value) {
+                this.mincolour = value;
+            }
+
+            /**
+             * Gets the value of the noValueColour property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link NoValueColour }
+             *     
+             */
+            public NoValueColour getNoValueColour() {
+                if (noValueColour == null) {
+                    return NoValueColour.MIN;
+                } else {
+                    return noValueColour;
+                }
+            }
+
+            /**
+             * Sets the value of the noValueColour property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link NoValueColour }
+             *     
+             */
+            public void setNoValueColour(NoValueColour value) {
+                this.noValueColour = value;
+            }
+
+            /**
+             * Gets the value of the threshold property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getThreshold() {
+                return threshold;
+            }
+
+            /**
+             * Sets the value of the threshold property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setThreshold(Float value) {
+                this.threshold = value;
+            }
+
+            /**
+             * Gets the value of the threshstate property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getThreshstate() {
+                return threshstate;
+            }
+
+            /**
+             * Sets the value of the threshstate property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setThreshstate(Integer value) {
+                this.threshstate = value;
+            }
+
+            /**
+             * Gets the value of the max property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getMax() {
+                return max;
+            }
+
+            /**
+             * Sets the value of the max property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setMax(Float value) {
+                this.max = value;
+            }
+
+            /**
+             * Gets the value of the min property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getMin() {
+                return min;
+            }
+
+            /**
+             * Sets the value of the min property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setMin(Float value) {
+                this.min = value;
+            }
+
+            /**
+             * Gets the value of the colourByLabel property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Boolean }
+             *     
+             */
+            public Boolean isColourByLabel() {
+                return colourByLabel;
+            }
+
+            /**
+             * Sets the value of the colourByLabel property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Boolean }
+             *     
+             */
+            public void setColourByLabel(Boolean value) {
+                this.colourByLabel = value;
+            }
+
+            /**
+             * Gets the value of the autoScale property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Boolean }
+             *     
+             */
+            public Boolean isAutoScale() {
+                return autoScale;
+            }
+
+            /**
+             * Sets the value of the autoScale property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Boolean }
+             *     
+             */
+            public void setAutoScale(Boolean value) {
+                this.autoScale = value;
+            }
 
-    /**
-     * Sets the value of the showSequenceLogo property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowSequenceLogo(Boolean value)
-    {
-      this.showSequenceLogo = value;
-    }
+        }
 
-    /**
-     * Gets the value of the normaliseSequenceLogo property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isNormaliseSequenceLogo()
-    {
-      if (normaliseSequenceLogo == null)
-      {
-        return false;
-      }
-      else
-      {
-        return normaliseSequenceLogo;
-      }
     }
 
-    /**
-     * Sets the value of the normaliseSequenceLogo property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setNormaliseSequenceLogo(Boolean value)
-    {
-      this.normaliseSequenceLogo = value;
-    }
 
     /**
-     * Gets the value of the id property.
+     * <p>Java class for anonymous complex type.
      * 
-     * @return possible object is {@link String }
+     * <p>The following schema fragment specifies the expected content contained within this class.
      * 
-     */
-    public String getId()
-    {
-      return id;
-    }
-
-    /**
-     * Sets the value of the id property.
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+     *         &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+     *       &lt;/sequence>
+     *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
      * 
-     * @param value
-     *          allowed object is {@link String }
      * 
      */
-    public void setId(String value)
-    {
-      this.id = value;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "seq",
+        "annotationColours"
+    })
+    public static class JGroup {
+
+        @XmlElement(namespace = "www.jalview.org", required = true)
+        protected List<String> seq;
+        @XmlElement(namespace = "www.jalview.org")
+        protected AnnotationColourScheme annotationColours;
+        @XmlAttribute(name = "start")
+        protected Integer start;
+        @XmlAttribute(name = "end")
+        protected Integer end;
+        @XmlAttribute(name = "name")
+        protected String name;
+        @XmlAttribute(name = "colour")
+        protected String colour;
+        @XmlAttribute(name = "consThreshold")
+        protected Integer consThreshold;
+        @XmlAttribute(name = "pidThreshold")
+        protected Integer pidThreshold;
+        @XmlAttribute(name = "outlineColour")
+        protected Integer outlineColour;
+        @XmlAttribute(name = "displayBoxes")
+        protected Boolean displayBoxes;
+        @XmlAttribute(name = "displayText")
+        protected Boolean displayText;
+        @XmlAttribute(name = "colourText")
+        protected Boolean colourText;
+        @XmlAttribute(name = "textCol1")
+        protected Integer textCol1;
+        @XmlAttribute(name = "textCol2")
+        protected Integer textCol2;
+        @XmlAttribute(name = "textColThreshold")
+        protected Integer textColThreshold;
+        @XmlAttribute(name = "showUnconserved")
+        protected Boolean showUnconserved;
+        @XmlAttribute(name = "ignoreGapsinConsensus")
+        protected Boolean ignoreGapsinConsensus;
+        @XmlAttribute(name = "showConsensusHistogram")
+        protected Boolean showConsensusHistogram;
+        @XmlAttribute(name = "showSequenceLogo")
+        protected Boolean showSequenceLogo;
+        @XmlAttribute(name = "normaliseSequenceLogo")
+        protected Boolean normaliseSequenceLogo;
+        @XmlAttribute(name = "id")
+        protected String id;
 
-  }
-
-  /**
-   * &lt;p&gt;Java class for anonymous complex type.
-   * 
-   * &lt;p&gt;The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-   * &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
-   * &amp;lt;sequence&amp;gt; &amp;lt;element name="features"
-   * type="{www.jalview.org}feature" maxOccurs="unbounded"
-   * minOccurs="0"/&amp;gt; &amp;lt;element name="pdbids" maxOccurs="unbounded"
-   * minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
-   * &amp;lt;complexContent&amp;gt; &amp;lt;extension
-   * base="{www.jalview.org}pdbentry"&amp;gt; &amp;lt;sequence&amp;gt;
-   * &amp;lt;element name="structureState" maxOccurs="unbounded"
-   * minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
-   * &amp;lt;simpleContent&amp;gt; &amp;lt;extension
-   * base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
-   * &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
-   * &amp;lt;attribute name="visible"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;attribute name="viewId"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
-   * name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean"
-   * default="true" /&amp;gt; &amp;lt;attribute name="colourwithAlignPanel"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
-   * &amp;lt;attribute name="colourByJmol"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
-   * &amp;lt;attribute name="type"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-   * &amp;lt;/extension&amp;gt; &amp;lt;/simpleContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
-   * &amp;lt;/sequence&amp;gt; &amp;lt;/extension&amp;gt;
-   * &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt;
-   * &amp;lt;/element&amp;gt; &amp;lt;element name="hiddenSequences"
-   * type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded"
-   * minOccurs="0"/&amp;gt; &amp;lt;element name="rnaViewer"
-   * maxOccurs="unbounded" minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
-   * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
-   * &amp;lt;sequence&amp;gt; &amp;lt;element name="secondaryStructure"
-   * maxOccurs="unbounded"&amp;gt; &amp;lt;complexType&amp;gt;
-   * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
-   * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-   * &amp;lt;attribute name="annotationId" use="required"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
-   * name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;attribute name="viewerState"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-   * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
-   * &amp;lt;/sequence&amp;gt; &amp;lt;attGroup
-   * ref="{www.jalview.org}swingwindow"/&amp;gt; &amp;lt;attribute name="title"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
-   * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-   * &amp;lt;attribute name="dividerLocation"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
-   * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
-   * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
-   * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="colour"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
-   * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
-   * /&amp;gt; &amp;lt;attribute name="end" use="required"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
-   * name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
-   * /&amp;gt; &amp;lt;attribute name="hidden"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;attribute name="viewreference"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(
-    name = "",
-    propOrder =
-    { "features", "pdbids", "hiddenSequences", "rnaViewer" })
-  public static class JSeq
-  {
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List<Feature> features;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List<JalviewModel.JSeq.Pdbids> pdbids;
-
-    @XmlElement(namespace = "www.jalview.org", type = Integer.class)
-    protected List<Integer> hiddenSequences;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
-
-    @XmlAttribute(name = "colour")
-    protected Integer colour;
-
-    @XmlAttribute(name = "start", required = true)
-    protected int start;
-
-    @XmlAttribute(name = "end", required = true)
-    protected int end;
-
-    @XmlAttribute(name = "id", required = true)
-    protected String id;
-
-    @XmlAttribute(name = "hidden")
-    protected Boolean hidden;
-
-    @XmlAttribute(name = "viewreference")
-    protected Boolean viewreference;
-
-    /**
-     * Gets the value of the features property.
-     * 
-     * &lt;p&gt; This accessor method returns a reference to the live list, not
-     * a snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * &lt;CODE&gt;set&lt;/CODE&gt; method for the features property.
-     * 
-     * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-     * getFeatures().add(newItem); &lt;/pre&gt;
-     * 
-     * 
-     * &lt;p&gt; Objects of the following type(s) are allowed in the list
-     * {@link Feature }
-     * 
-     * 
-     */
-    public List<Feature> getFeatures()
-    {
-      if (features == null)
-      {
-        features = new ArrayList<Feature>();
-      }
-      return this.features;
-    }
-
-    /**
-     * Gets the value of the pdbids property.
-     * 
-     * &lt;p&gt; This accessor method returns a reference to the live list, not
-     * a snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * &lt;CODE&gt;set&lt;/CODE&gt; method for the pdbids property.
-     * 
-     * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-     * getPdbids().add(newItem); &lt;/pre&gt;
-     * 
-     * 
-     * &lt;p&gt; Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.JSeq.Pdbids }
-     * 
-     * 
-     */
-    public List<JalviewModel.JSeq.Pdbids> getPdbids()
-    {
-      if (pdbids == null)
-      {
-        pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
-      }
-      return this.pdbids;
-    }
-
-    /**
-     * Gets the value of the hiddenSequences property.
-     * 
-     * &lt;p&gt; This accessor method returns a reference to the live list, not
-     * a snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * &lt;CODE&gt;set&lt;/CODE&gt; method for the hiddenSequences property.
-     * 
-     * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-     * getHiddenSequences().add(newItem); &lt;/pre&gt;
-     * 
-     * 
-     * &lt;p&gt; Objects of the following type(s) are allowed in the list
-     * {@link Integer }
-     * 
-     * 
-     */
-    public List<Integer> getHiddenSequences()
-    {
-      if (hiddenSequences == null)
-      {
-        hiddenSequences = new ArrayList<Integer>();
-      }
-      return this.hiddenSequences;
-    }
-
-    /**
-     * Gets the value of the rnaViewer property.
-     * 
-     * &lt;p&gt; This accessor method returns a reference to the live list, not
-     * a snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * &lt;CODE&gt;set&lt;/CODE&gt; method for the rnaViewer property.
-     * 
-     * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-     * getRnaViewer().add(newItem); &lt;/pre&gt;
-     * 
-     * 
-     * &lt;p&gt; Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.JSeq.RnaViewer }
-     * 
-     * 
-     */
-    public List<JalviewModel.JSeq.RnaViewer> getRnaViewer()
-    {
-      if (rnaViewer == null)
-      {
-        rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
-      }
-      return this.rnaViewer;
-    }
-
-    /**
-     * Gets the value of the colour property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getColour()
-    {
-      return colour;
-    }
-
-    /**
-     * Sets the value of the colour property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setColour(Integer value)
-    {
-      this.colour = value;
-    }
-
-    /**
-     * Gets the value of the start property.
-     * 
-     */
-    public int getStart()
-    {
-      return start;
-    }
-
-    /**
-     * Sets the value of the start property.
-     * 
-     */
-    public void setStart(int value)
-    {
-      this.start = value;
-    }
-
-    /**
-     * Gets the value of the end property.
-     * 
-     */
-    public int getEnd()
-    {
-      return end;
-    }
-
-    /**
-     * Sets the value of the end property.
-     * 
-     */
-    public void setEnd(int value)
-    {
-      this.end = value;
-    }
-
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getId()
-    {
-      return id;
-    }
-
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setId(String value)
-    {
-      this.id = value;
-    }
-
-    /**
-     * Gets the value of the hidden property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isHidden()
-    {
-      return hidden;
-    }
-
-    /**
-     * Sets the value of the hidden property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setHidden(Boolean value)
-    {
-      this.hidden = value;
-    }
-
-    /**
-     * Gets the value of the viewreference property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isViewreference()
-    {
-      return viewreference;
-    }
-
-    /**
-     * Sets the value of the viewreference property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setViewreference(Boolean value)
-    {
-      this.viewreference = value;
-    }
-
-    /**
-     * &lt;p&gt;Java class for anonymous complex type.
-     * 
-     * &lt;p&gt;The following schema fragment specifies the expected content
-     * contained within this class.
-     * 
-     * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-     * &amp;lt;extension base="{www.jalview.org}pdbentry"&amp;gt;
-     * &amp;lt;sequence&amp;gt; &amp;lt;element name="structureState"
-     * maxOccurs="unbounded" minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
-     * &amp;lt;simpleContent&amp;gt; &amp;lt;extension
-     * base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
-     * &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
-     * &amp;lt;attribute name="visible"
-     * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-     * &amp;lt;attribute name="viewId"
-     * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-     * &amp;lt;attribute name="alignwithAlignPanel"
-     * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
-     * &amp;lt;attribute name="colourwithAlignPanel"
-     * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
-     * /&amp;gt; &amp;lt;attribute name="colourByJmol"
-     * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
-     * &amp;lt;attribute name="type"
-     * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-     * &amp;lt;/extension&amp;gt; &amp;lt;/simpleContent&amp;gt;
-     * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
-     * &amp;lt;/sequence&amp;gt; &amp;lt;/extension&amp;gt;
-     * &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = { "structureState" })
-    public static class Pdbids extends Pdbentry
-    {
-
-      @XmlElement(namespace = "www.jalview.org")
-      protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
-
-      /**
-       * Gets the value of the structureState property.
-       * 
-       * &lt;p&gt; This accessor method returns a reference to the live list,
-       * not a snapshot. Therefore any modification you make to the returned
-       * list will be present inside the JAXB object. This is why there is not a
-       * &lt;CODE&gt;set&lt;/CODE&gt; method for the structureState property.
-       * 
-       * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-       * getStructureState().add(newItem); &lt;/pre&gt;
-       * 
-       * 
-       * &lt;p&gt; Objects of the following type(s) are allowed in the list
-       * {@link JalviewModel.JSeq.Pdbids.StructureState }
-       * 
-       * 
-       */
-      public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState()
-      {
-        if (structureState == null)
-        {
-          structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
-        }
-        return this.structureState;
-      }
-
-      /**
-       * &lt;p&gt;Java class for anonymous complex type.
-       * 
-       * &lt;p&gt;The following schema fragment specifies the expected content
-       * contained within this class.
-       * 
-       * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;simpleContent&amp;gt;
-       * &amp;lt;extension
-       * base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
-       * &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
-       * &amp;lt;attribute name="visible"
-       * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-       * &amp;lt;attribute name="viewId"
-       * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-       * &amp;lt;attribute name="alignwithAlignPanel"
-       * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true"
-       * /&amp;gt; &amp;lt;attribute name="colourwithAlignPanel"
-       * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
-       * /&amp;gt; &amp;lt;attribute name="colourByJmol"
-       * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true"
-       * /&amp;gt; &amp;lt;attribute name="type"
-       * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-       * &amp;lt;/extension&amp;gt; &amp;lt;/simpleContent&amp;gt;
-       * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-       * 
-       * 
-       */
-      @XmlAccessorType(XmlAccessType.FIELD)
-      @XmlType(name = "", propOrder = { "value" })
-      public static class StructureState
-      {
-
-        @XmlValue
-        protected String value;
-
-        @XmlAttribute(name = "visible")
-        protected Boolean visible;
-
-        @XmlAttribute(name = "viewId")
-        protected String viewId;
-
-        @XmlAttribute(name = "alignwithAlignPanel")
-        protected Boolean alignwithAlignPanel;
-
-        @XmlAttribute(name = "colourwithAlignPanel")
-        protected Boolean colourwithAlignPanel;
-
-        @XmlAttribute(name = "colourByJmol")
-        protected Boolean colourByJmol;
-
-        @XmlAttribute(name = "type")
-        protected String type;
-
-        @XmlAttribute(name = "width")
-        protected Integer width;
-
-        @XmlAttribute(name = "height")
-        protected Integer height;
-
-        @XmlAttribute(name = "xpos")
-        protected Integer xpos;
-
-        @XmlAttribute(name = "ypos")
-        protected Integer ypos;
+        /**
+         * Gets the value of the seq property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the seq property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getSeq().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link String }
+         * 
+         * 
+         */
+        public List<String> getSeq() {
+            if (seq == null) {
+                seq = new ArrayList<String>();
+            }
+            return this.seq;
+        }
 
         /**
-         * Gets the value of the value property.
-         * 
-         * @return possible object is {@link String }
+         * Gets the value of the annotationColours property.
          * 
+         * @return
+         *     possible object is
+         *     {@link AnnotationColourScheme }
+         *     
          */
-        public String getValue()
-        {
-          return value;
+        public AnnotationColourScheme getAnnotationColours() {
+            return annotationColours;
         }
 
         /**
-         * Sets the value of the value property.
+         * Sets the value of the annotationColours property.
          * 
          * @param value
-         *          allowed object is {@link String }
-         * 
+         *     allowed object is
+         *     {@link AnnotationColourScheme }
+         *     
          */
-        public void setValue(String value)
-        {
-          this.value = value;
+        public void setAnnotationColours(AnnotationColourScheme value) {
+            this.annotationColours = value;
         }
 
         /**
-         * Gets the value of the visible property.
-         * 
-         * @return possible object is {@link Boolean }
+         * Gets the value of the start property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
          */
-        public Boolean isVisible()
-        {
-          return visible;
+        public Integer getStart() {
+            return start;
         }
 
         /**
-         * Sets the value of the visible property.
+         * Sets the value of the start property.
          * 
          * @param value
-         *          allowed object is {@link Boolean }
-         * 
+         *     allowed object is
+         *     {@link Integer }
+         *     
          */
-        public void setVisible(Boolean value)
-        {
-          this.visible = value;
+        public void setStart(Integer value) {
+            this.start = value;
         }
 
         /**
-         * Gets the value of the viewId property.
-         * 
-         * @return possible object is {@link String }
+         * Gets the value of the end property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
          */
-        public String getViewId()
-        {
-          return viewId;
+        public Integer getEnd() {
+            return end;
         }
 
         /**
-         * Sets the value of the viewId property.
+         * Sets the value of the end property.
          * 
          * @param value
-         *          allowed object is {@link String }
-         * 
+         *     allowed object is
+         *     {@link Integer }
+         *     
          */
-        public void setViewId(String value)
-        {
-          this.viewId = value;
+        public void setEnd(Integer value) {
+            this.end = value;
         }
 
         /**
-         * Gets the value of the alignwithAlignPanel property.
-         * 
-         * @return possible object is {@link Boolean }
+         * Gets the value of the name property.
          * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
          */
-        public boolean isAlignwithAlignPanel()
-        {
-          if (alignwithAlignPanel == null)
-          {
-            return true;
-          }
-          else
-          {
-            return alignwithAlignPanel;
-          }
+        public String getName() {
+            return name;
         }
 
         /**
-         * Sets the value of the alignwithAlignPanel property.
+         * Sets the value of the name property.
          * 
          * @param value
-         *          allowed object is {@link Boolean }
-         * 
+         *     allowed object is
+         *     {@link String }
+         *     
          */
-        public void setAlignwithAlignPanel(Boolean value)
-        {
-          this.alignwithAlignPanel = value;
+        public void setName(String value) {
+            this.name = value;
         }
 
         /**
-         * Gets the value of the colourwithAlignPanel property.
-         * 
-         * @return possible object is {@link Boolean }
+         * Gets the value of the colour property.
          * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
          */
-        public boolean isColourwithAlignPanel()
-        {
-          if (colourwithAlignPanel == null)
-          {
-            return false;
-          }
-          else
-          {
-            return colourwithAlignPanel;
-          }
+        public String getColour() {
+            return colour;
         }
 
         /**
-         * Sets the value of the colourwithAlignPanel property.
+         * Sets the value of the colour property.
          * 
          * @param value
-         *          allowed object is {@link Boolean }
-         * 
+         *     allowed object is
+         *     {@link String }
+         *     
          */
-        public void setColourwithAlignPanel(Boolean value)
-        {
-          this.colourwithAlignPanel = value;
+        public void setColour(String value) {
+            this.colour = value;
         }
 
         /**
-         * Gets the value of the colourByJmol property.
-         * 
-         * @return possible object is {@link Boolean }
+         * Gets the value of the consThreshold property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
          */
-        public boolean isColourByJmol()
-        {
-          if (colourByJmol == null)
-          {
-            return true;
-          }
-          else
-          {
-            return colourByJmol;
-          }
+        public Integer getConsThreshold() {
+            return consThreshold;
         }
 
         /**
-         * Sets the value of the colourByJmol property.
+         * Sets the value of the consThreshold property.
          * 
          * @param value
-         *          allowed object is {@link Boolean }
-         * 
+         *     allowed object is
+         *     {@link Integer }
+         *     
          */
-        public void setColourByJmol(Boolean value)
-        {
-          this.colourByJmol = value;
+        public void setConsThreshold(Integer value) {
+            this.consThreshold = value;
         }
 
         /**
-         * Gets the value of the type property.
-         * 
-         * @return possible object is {@link String }
+         * Gets the value of the pidThreshold property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
          */
-        public String getType()
-        {
-          return type;
+        public Integer getPidThreshold() {
+            return pidThreshold;
         }
 
         /**
-         * Sets the value of the type property.
+         * Sets the value of the pidThreshold property.
          * 
          * @param value
-         *          allowed object is {@link String }
-         * 
+         *     allowed object is
+         *     {@link Integer }
+         *     
          */
-        public void setType(String value)
-        {
-          this.type = value;
+        public void setPidThreshold(Integer value) {
+            this.pidThreshold = value;
         }
 
         /**
-         * Gets the value of the width property.
-         * 
-         * @return possible object is {@link Integer }
+         * Gets the value of the outlineColour property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
          */
-        public Integer getWidth()
-        {
-          return width;
+        public Integer getOutlineColour() {
+            return outlineColour;
         }
 
         /**
-         * Sets the value of the width property.
+         * Sets the value of the outlineColour property.
          * 
          * @param value
-         *          allowed object is {@link Integer }
-         * 
+         *     allowed object is
+         *     {@link Integer }
+         *     
          */
-        public void setWidth(Integer value)
-        {
-          this.width = value;
+        public void setOutlineColour(Integer value) {
+            this.outlineColour = value;
         }
 
         /**
-         * Gets the value of the height property.
-         * 
-         * @return possible object is {@link Integer }
+         * Gets the value of the displayBoxes property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
          */
-        public Integer getHeight()
-        {
-          return height;
+        public Boolean isDisplayBoxes() {
+            return displayBoxes;
         }
 
         /**
-         * Sets the value of the height property.
+         * Sets the value of the displayBoxes property.
          * 
          * @param value
-         *          allowed object is {@link Integer }
-         * 
+         *     allowed object is
+         *     {@link Boolean }
+         *     
          */
-        public void setHeight(Integer value)
-        {
-          this.height = value;
+        public void setDisplayBoxes(Boolean value) {
+            this.displayBoxes = value;
         }
 
         /**
-         * Gets the value of the xpos property.
-         * 
-         * @return possible object is {@link Integer }
+         * Gets the value of the displayText property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
          */
-        public Integer getXpos()
-        {
-          return xpos;
+        public Boolean isDisplayText() {
+            return displayText;
         }
 
         /**
-         * Sets the value of the xpos property.
+         * Sets the value of the displayText property.
          * 
          * @param value
-         *          allowed object is {@link Integer }
-         * 
+         *     allowed object is
+         *     {@link Boolean }
+         *     
          */
-        public void setXpos(Integer value)
-        {
-          this.xpos = value;
+        public void setDisplayText(Boolean value) {
+            this.displayText = value;
         }
 
         /**
-         * Gets the value of the ypos property.
-         * 
-         * @return possible object is {@link Integer }
+         * Gets the value of the colourText property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
          */
-        public Integer getYpos()
-        {
-          return ypos;
+        public Boolean isColourText() {
+            return colourText;
         }
 
         /**
-         * Sets the value of the ypos property.
+         * Sets the value of the colourText property.
          * 
          * @param value
-         *          allowed object is {@link Integer }
-         * 
+         *     allowed object is
+         *     {@link Boolean }
+         *     
          */
-        public void setYpos(Integer value)
-        {
-          this.ypos = value;
+        public void setColourText(Boolean value) {
+            this.colourText = value;
         }
 
-      }
-
-    }
-
-    /**
-     * &lt;p&gt;Java class for anonymous complex type.
-     * 
-     * &lt;p&gt;The following schema fragment specifies the expected content
-     * contained within this class.
-     * 
-     * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-     * &amp;lt;restriction
-     * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
-     * &amp;lt;sequence&amp;gt; &amp;lt;element name="secondaryStructure"
-     * maxOccurs="unbounded"&amp;gt; &amp;lt;complexType&amp;gt;
-     * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
-     * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
-     * &amp;lt;attribute name="title"
-     * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-     * &amp;lt;attribute name="annotationId" use="required"
-     * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-     * &amp;lt;attribute name="gapped"
-     * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-     * &amp;lt;attribute name="viewerState"
-     * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-     * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-     * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
-     * &amp;lt;/sequence&amp;gt; &amp;lt;attGroup
-     * ref="{www.jalview.org}swingwindow"/&amp;gt; &amp;lt;attribute
-     * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-     * &amp;lt;attribute name="viewId"
-     * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-     * &amp;lt;attribute name="dividerLocation"
-     * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
-     * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
-     * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-     * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = { "secondaryStructure" })
-    public static class RnaViewer
-    {
-
-      @XmlElement(namespace = "www.jalview.org", required = true)
-      protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
-
-      @XmlAttribute(name = "title")
-      protected String title;
-
-      @XmlAttribute(name = "viewId")
-      protected String viewId;
-
-      @XmlAttribute(name = "dividerLocation")
-      protected Integer dividerLocation;
-
-      @XmlAttribute(name = "selectedRna")
-      protected Integer selectedRna;
-
-      @XmlAttribute(name = "width")
-      protected Integer width;
-
-      @XmlAttribute(name = "height")
-      protected Integer height;
-
-      @XmlAttribute(name = "xpos")
-      protected Integer xpos;
-
-      @XmlAttribute(name = "ypos")
-      protected Integer ypos;
-
-      /**
-       * Gets the value of the secondaryStructure property.
-       * 
-       * &lt;p&gt; This accessor method returns a reference to the live list,
-       * not a snapshot. Therefore any modification you make to the returned
-       * list will be present inside the JAXB object. This is why there is not a
-       * &lt;CODE&gt;set&lt;/CODE&gt; method for the secondaryStructure
-       * property.
-       * 
-       * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-       * getSecondaryStructure().add(newItem); &lt;/pre&gt;
-       * 
-       * 
-       * &lt;p&gt; Objects of the following type(s) are allowed in the list
-       * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
-       * 
-       * 
-       */
-      public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure()
-      {
-        if (secondaryStructure == null)
-        {
-          secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
-        }
-        return this.secondaryStructure;
-      }
-
-      /**
-       * Gets the value of the title property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getTitle()
-      {
-        return title;
-      }
-
-      /**
-       * Sets the value of the title property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setTitle(String value)
-      {
-        this.title = value;
-      }
-
-      /**
-       * Gets the value of the viewId property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getViewId()
-      {
-        return viewId;
-      }
-
-      /**
-       * Sets the value of the viewId property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setViewId(String value)
-      {
-        this.viewId = value;
-      }
-
-      /**
-       * Gets the value of the dividerLocation property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getDividerLocation()
-      {
-        return dividerLocation;
-      }
-
-      /**
-       * Sets the value of the dividerLocation property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setDividerLocation(Integer value)
-      {
-        this.dividerLocation = value;
-      }
-
-      /**
-       * Gets the value of the selectedRna property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getSelectedRna()
-      {
-        return selectedRna;
-      }
-
-      /**
-       * Sets the value of the selectedRna property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setSelectedRna(Integer value)
-      {
-        this.selectedRna = value;
-      }
-
-      /**
-       * Gets the value of the width property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getWidth()
-      {
-        return width;
-      }
-
-      /**
-       * Sets the value of the width property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setWidth(Integer value)
-      {
-        this.width = value;
-      }
-
-      /**
-       * Gets the value of the height property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getHeight()
-      {
-        return height;
-      }
-
-      /**
-       * Sets the value of the height property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setHeight(Integer value)
-      {
-        this.height = value;
-      }
-
-      /**
-       * Gets the value of the xpos property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getXpos()
-      {
-        return xpos;
-      }
-
-      /**
-       * Sets the value of the xpos property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setXpos(Integer value)
-      {
-        this.xpos = value;
-      }
-
-      /**
-       * Gets the value of the ypos property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getYpos()
-      {
-        return ypos;
-      }
-
-      /**
-       * Sets the value of the ypos property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setYpos(Integer value)
-      {
-        this.ypos = value;
-      }
-
-      /**
-       * &lt;p&gt;Java class for anonymous complex type.
-       * 
-       * &lt;p&gt;The following schema fragment specifies the expected content
-       * contained within this class.
-       * 
-       * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-       * &amp;lt;restriction
-       * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
-       * &amp;lt;attribute name="title"
-       * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-       * &amp;lt;attribute name="annotationId" use="required"
-       * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-       * &amp;lt;attribute name="gapped"
-       * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-       * &amp;lt;attribute name="viewerState"
-       * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-       * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-       * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-       * 
-       * 
-       */
-      @XmlAccessorType(XmlAccessType.FIELD)
-      @XmlType(name = "")
-      public static class SecondaryStructure
-      {
-
-        @XmlAttribute(name = "title")
-        protected String title;
-
-        @XmlAttribute(name = "annotationId", required = true)
-        protected String annotationId;
-
-        @XmlAttribute(name = "gapped")
-        protected Boolean gapped;
-
-        @XmlAttribute(name = "viewerState")
-        protected String viewerState;
+        /**
+         * Gets the value of the textCol1 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getTextCol1() {
+            return textCol1;
+        }
 
         /**
-         * Gets the value of the title property.
+         * Sets the value of the textCol1 property.
          * 
-         * @return possible object is {@link String }
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setTextCol1(Integer value) {
+            this.textCol1 = value;
+        }
+
+        /**
+         * Gets the value of the textCol2 property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
          */
-        public String getTitle()
-        {
-          return title;
+        public Integer getTextCol2() {
+            return textCol2;
         }
 
         /**
-         * Sets the value of the title property.
+         * Sets the value of the textCol2 property.
          * 
          * @param value
-         *          allowed object is {@link String }
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setTextCol2(Integer value) {
+            this.textCol2 = value;
+        }
+
+        /**
+         * Gets the value of the textColThreshold property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
          */
-        public void setTitle(String value)
-        {
-          this.title = value;
+        public Integer getTextColThreshold() {
+            return textColThreshold;
         }
 
         /**
-         * Gets the value of the annotationId property.
+         * Sets the value of the textColThreshold property.
          * 
-         * @return possible object is {@link String }
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setTextColThreshold(Integer value) {
+            this.textColThreshold = value;
+        }
+
+        /**
+         * Gets the value of the showUnconserved property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
          */
-        public String getAnnotationId()
-        {
-          return annotationId;
+        public Boolean isShowUnconserved() {
+            return showUnconserved;
         }
 
         /**
-         * Sets the value of the annotationId property.
+         * Sets the value of the showUnconserved property.
          * 
          * @param value
-         *          allowed object is {@link String }
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowUnconserved(Boolean value) {
+            this.showUnconserved = value;
+        }
+
+        /**
+         * Gets the value of the ignoreGapsinConsensus property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
          */
-        public void setAnnotationId(String value)
-        {
-          this.annotationId = value;
+        public boolean isIgnoreGapsinConsensus() {
+            if (ignoreGapsinConsensus == null) {
+                return true;
+            } else {
+                return ignoreGapsinConsensus;
+            }
         }
 
         /**
-         * Gets the value of the gapped property.
+         * Sets the value of the ignoreGapsinConsensus property.
          * 
-         * @return possible object is {@link Boolean }
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setIgnoreGapsinConsensus(Boolean value) {
+            this.ignoreGapsinConsensus = value;
+        }
+
+        /**
+         * Gets the value of the showConsensusHistogram property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
          */
-        public Boolean isGapped()
-        {
-          return gapped;
+        public boolean isShowConsensusHistogram() {
+            if (showConsensusHistogram == null) {
+                return true;
+            } else {
+                return showConsensusHistogram;
+            }
         }
 
         /**
-         * Sets the value of the gapped property.
+         * Sets the value of the showConsensusHistogram property.
          * 
          * @param value
-         *          allowed object is {@link Boolean }
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowConsensusHistogram(Boolean value) {
+            this.showConsensusHistogram = value;
+        }
+
+        /**
+         * Gets the value of the showSequenceLogo property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
          */
-        public void setGapped(Boolean value)
-        {
-          this.gapped = value;
+        public boolean isShowSequenceLogo() {
+            if (showSequenceLogo == null) {
+                return false;
+            } else {
+                return showSequenceLogo;
+            }
         }
 
         /**
-         * Gets the value of the viewerState property.
+         * Sets the value of the showSequenceLogo property.
          * 
-         * @return possible object is {@link String }
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowSequenceLogo(Boolean value) {
+            this.showSequenceLogo = value;
+        }
+
+        /**
+         * Gets the value of the normaliseSequenceLogo property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
          */
-        public String getViewerState()
-        {
-          return viewerState;
+        public boolean isNormaliseSequenceLogo() {
+            if (normaliseSequenceLogo == null) {
+                return false;
+            } else {
+                return normaliseSequenceLogo;
+            }
         }
 
         /**
-         * Sets the value of the viewerState property.
+         * Sets the value of the normaliseSequenceLogo property.
          * 
          * @param value
-         *          allowed object is {@link String }
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setNormaliseSequenceLogo(Boolean value) {
+            this.normaliseSequenceLogo = value;
+        }
+
+        /**
+         * Gets the value of the id property.
          * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
          */
-        public void setViewerState(String value)
-        {
-          this.viewerState = value;
+        public String getId() {
+            return id;
         }
 
-      }
+        /**
+         * Sets the value of the id property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setId(String value) {
+            this.id = value;
+        }
 
     }
 
-  }
-
-  /**
-   * &lt;p&gt;Java class for anonymous complex type.
-   * 
-   * &lt;p&gt;The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-   * &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
-   * &amp;lt;sequence&amp;gt; &amp;lt;element name="sequencePoint"
-   * maxOccurs="unbounded"&amp;gt; &amp;lt;complexType&amp;gt;
-   * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
-   * ref="{www.jalview.org}position"/&amp;gt; &amp;lt;attribute
-   * name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string"
-   * /&amp;gt; &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
-   * name="axis" maxOccurs="3" minOccurs="3"&amp;gt; &amp;lt;complexType&amp;gt;
-   * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
-   * ref="{www.jalview.org}position"/&amp;gt; &amp;lt;/restriction&amp;gt;
-   * &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt;
-   * &amp;lt;/element&amp;gt; &amp;lt;element name="seqPointMin"&amp;gt;
-   * &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-   * &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
-   * ref="{www.jalview.org}position"/&amp;gt; &amp;lt;/restriction&amp;gt;
-   * &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt;
-   * &amp;lt;/element&amp;gt; &amp;lt;element name="seqPointMax"&amp;gt;
-   * &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-   * &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
-   * ref="{www.jalview.org}position"/&amp;gt; &amp;lt;/restriction&amp;gt;
-   * &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt;
-   * &amp;lt;/element&amp;gt; &amp;lt;element name="pcaData"
-   * type="{www.jalview.org}PcaDataType"/&amp;gt; &amp;lt;/sequence&amp;gt;
-   * &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
-   * &amp;lt;attGroup ref="{www.jalview.org}SimilarityParams"/&amp;gt;
-   * &amp;lt;attribute name="title"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
-   * name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string"
-   * /&amp;gt; &amp;lt;attribute name="xDim"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
-   * name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
-   * &amp;lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int"
-   * /&amp;gt; &amp;lt;attribute name="bgColour"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
-   * name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
-   * &amp;lt;attribute name="showLabels"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;attribute name="linkToAllViews"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(
-    name = "",
-    propOrder =
-    { "sequencePoint", "axis", "seqPointMin", "seqPointMax", "pcaData" })
-  public static class PcaViewer
-  {
-
-    @XmlElement(namespace = "www.jalview.org", required = true)
-    protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
-
-    @XmlElement(namespace = "www.jalview.org", required = true)
-    protected List<JalviewModel.PcaViewer.Axis> axis;
-
-    @XmlElement(namespace = "www.jalview.org", required = true)
-    protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
-
-    @XmlElement(namespace = "www.jalview.org", required = true)
-    protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
-
-    @XmlElement(namespace = "www.jalview.org", required = true)
-    protected PcaDataType pcaData;
-
-    @XmlAttribute(name = "title")
-    protected String title;
-
-    @XmlAttribute(name = "scoreModelName")
-    protected String scoreModelName;
-
-    @XmlAttribute(name = "xDim")
-    protected Integer xDim;
-
-    @XmlAttribute(name = "yDim")
-    protected Integer yDim;
-
-    @XmlAttribute(name = "zDim")
-    protected Integer zDim;
-
-    @XmlAttribute(name = "bgColour")
-    protected Integer bgColour;
-
-    @XmlAttribute(name = "scaleFactor")
-    protected Float scaleFactor;
-
-    @XmlAttribute(name = "showLabels")
-    protected Boolean showLabels;
-
-    @XmlAttribute(name = "linkToAllViews")
-    protected Boolean linkToAllViews;
-
-    @XmlAttribute(name = "width")
-    protected Integer width;
-
-    @XmlAttribute(name = "height")
-    protected Integer height;
-
-    @XmlAttribute(name = "xpos")
-    protected Integer xpos;
-
-    @XmlAttribute(name = "ypos")
-    protected Integer ypos;
-
-    @XmlAttribute(name = "includeGaps")
-    protected Boolean includeGaps;
-
-    @XmlAttribute(name = "matchGaps")
-    protected Boolean matchGaps;
-
-    @XmlAttribute(name = "includeGappedColumns")
-    protected Boolean includeGappedColumns;
-
-    @XmlAttribute(name = "denominateByShortestLength")
-    protected Boolean denominateByShortestLength;
 
     /**
-     * Gets the value of the sequencePoint property.
-     * 
-     * &lt;p&gt; This accessor method returns a reference to the live list, not
-     * a snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * &lt;CODE&gt;set&lt;/CODE&gt; method for the sequencePoint property.
-     * 
-     * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-     * getSequencePoint().add(newItem); &lt;/pre&gt;
-     * 
-     * 
-     * &lt;p&gt; Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.PcaViewer.SequencePoint }
-     * 
-     * 
-     */
-    public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint()
-    {
-      if (sequencePoint == null)
-      {
-        sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
-      }
-      return this.sequencePoint;
-    }
-
-    /**
-     * Gets the value of the axis property.
-     * 
-     * &lt;p&gt; This accessor method returns a reference to the live list, not
-     * a snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * &lt;CODE&gt;set&lt;/CODE&gt; method for the axis property.
-     * 
-     * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-     * getAxis().add(newItem); &lt;/pre&gt;
-     * 
-     * 
-     * &lt;p&gt; Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.PcaViewer.Axis }
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+     *         &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;extension base="{www.jalview.org}pdbentry">
+     *                 &lt;sequence>
+     *                   &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
+     *                     &lt;complexType>
+     *                       &lt;simpleContent>
+     *                         &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
+     *                           &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+     *                           &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                           &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                           &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *                           &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *                           &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *                           &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                         &lt;/extension>
+     *                       &lt;/simpleContent>
+     *                     &lt;/complexType>
+     *                   &lt;/element>
+     *                 &lt;/sequence>
+     *               &lt;/extension>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *         &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+     *         &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 &lt;sequence>
+     *                   &lt;element name="secondaryStructure" maxOccurs="unbounded">
+     *                     &lt;complexType>
+     *                       &lt;complexContent>
+     *                         &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                           &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                           &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                           &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                           &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                         &lt;/restriction>
+     *                       &lt;/complexContent>
+     *                     &lt;/complexType>
+     *                   &lt;/element>
+     *                 &lt;/sequence>
+     *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+     *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *               &lt;/restriction>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *       &lt;/sequence>
+     *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
      * 
      * 
      */
-    public List<JalviewModel.PcaViewer.Axis> getAxis()
-    {
-      if (axis == null)
-      {
-        axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
-      }
-      return this.axis;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "features",
+        "pdbids",
+        "hiddenSequences",
+        "rnaViewer"
+    })
+    public static class JSeq {
+
+        @XmlElement(namespace = "www.jalview.org")
+        protected List<Feature> features;
+        @XmlElement(namespace = "www.jalview.org")
+        protected List<JalviewModel.JSeq.Pdbids> pdbids;
+        @XmlElement(namespace = "www.jalview.org", type = Integer.class)
+        protected List<Integer> hiddenSequences;
+        @XmlElement(namespace = "www.jalview.org")
+        protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
+        @XmlAttribute(name = "colour")
+        protected Integer colour;
+        @XmlAttribute(name = "start", required = true)
+        protected int start;
+        @XmlAttribute(name = "end", required = true)
+        protected int end;
+        @XmlAttribute(name = "id", required = true)
+        protected String id;
+        @XmlAttribute(name = "hidden")
+        protected Boolean hidden;
+        @XmlAttribute(name = "viewreference")
+        protected Boolean viewreference;
 
-    /**
-     * Gets the value of the seqPointMin property.
-     * 
-     * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMin }
-     * 
-     */
-    public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin()
-    {
-      return seqPointMin;
-    }
+        /**
+         * Gets the value of the features property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the features property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getFeatures().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link Feature }
+         * 
+         * 
+         */
+        public List<Feature> getFeatures() {
+            if (features == null) {
+                features = new ArrayList<Feature>();
+            }
+            return this.features;
+        }
 
-    /**
-     * Sets the value of the seqPointMin property.
-     * 
-     * @param value
-     *          allowed object is {@link JalviewModel.PcaViewer.SeqPointMin }
-     * 
-     */
-    public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value)
-    {
-      this.seqPointMin = value;
-    }
+        /**
+         * Gets the value of the pdbids property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the pdbids property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getPdbids().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.JSeq.Pdbids }
+         * 
+         * 
+         */
+        public List<JalviewModel.JSeq.Pdbids> getPdbids() {
+            if (pdbids == null) {
+                pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
+            }
+            return this.pdbids;
+        }
 
-    /**
-     * Gets the value of the seqPointMax property.
-     * 
-     * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMax }
-     * 
-     */
-    public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax()
-    {
-      return seqPointMax;
-    }
+        /**
+         * Gets the value of the hiddenSequences property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getHiddenSequences().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link Integer }
+         * 
+         * 
+         */
+        public List<Integer> getHiddenSequences() {
+            if (hiddenSequences == null) {
+                hiddenSequences = new ArrayList<Integer>();
+            }
+            return this.hiddenSequences;
+        }
 
-    /**
-     * Sets the value of the seqPointMax property.
-     * 
-     * @param value
-     *          allowed object is {@link JalviewModel.PcaViewer.SeqPointMax }
-     * 
-     */
-    public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value)
-    {
-      this.seqPointMax = value;
-    }
+        /**
+         * Gets the value of the rnaViewer property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getRnaViewer().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.JSeq.RnaViewer }
+         * 
+         * 
+         */
+        public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
+            if (rnaViewer == null) {
+                rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
+            }
+            return this.rnaViewer;
+        }
 
-    /**
-     * Gets the value of the pcaData property.
-     * 
-     * @return possible object is {@link PcaDataType }
-     * 
-     */
-    public PcaDataType getPcaData()
-    {
-      return pcaData;
-    }
+        /**
+         * Gets the value of the colour property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getColour() {
+            return colour;
+        }
 
-    /**
-     * Sets the value of the pcaData property.
-     * 
-     * @param value
-     *          allowed object is {@link PcaDataType }
-     * 
-     */
-    public void setPcaData(PcaDataType value)
-    {
-      this.pcaData = value;
-    }
+        /**
+         * Sets the value of the colour property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setColour(Integer value) {
+            this.colour = value;
+        }
 
-    /**
-     * Gets the value of the title property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getTitle()
-    {
-      return title;
-    }
+        /**
+         * Gets the value of the start property.
+         * 
+         */
+        public int getStart() {
+            return start;
+        }
 
-    /**
-     * Sets the value of the title property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setTitle(String value)
-    {
-      this.title = value;
-    }
+        /**
+         * Sets the value of the start property.
+         * 
+         */
+        public void setStart(int value) {
+            this.start = value;
+        }
 
-    /**
-     * Gets the value of the scoreModelName property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getScoreModelName()
-    {
-      return scoreModelName;
-    }
+        /**
+         * Gets the value of the end property.
+         * 
+         */
+        public int getEnd() {
+            return end;
+        }
 
-    /**
-     * Sets the value of the scoreModelName property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setScoreModelName(String value)
-    {
-      this.scoreModelName = value;
-    }
+        /**
+         * Sets the value of the end property.
+         * 
+         */
+        public void setEnd(int value) {
+            this.end = value;
+        }
 
-    /**
-     * Gets the value of the xDim property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getXDim()
-    {
-      return xDim;
-    }
+        /**
+         * Gets the value of the id property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getId() {
+            return id;
+        }
 
-    /**
-     * Sets the value of the xDim property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setXDim(Integer value)
-    {
-      this.xDim = value;
-    }
+        /**
+         * Sets the value of the id property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setId(String value) {
+            this.id = value;
+        }
 
-    /**
-     * Gets the value of the yDim property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getYDim()
-    {
-      return yDim;
-    }
+        /**
+         * Gets the value of the hidden property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isHidden() {
+            return hidden;
+        }
 
-    /**
-     * Sets the value of the yDim property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setYDim(Integer value)
-    {
-      this.yDim = value;
-    }
+        /**
+         * Sets the value of the hidden property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setHidden(Boolean value) {
+            this.hidden = value;
+        }
 
-    /**
-     * Gets the value of the zDim property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getZDim()
-    {
-      return zDim;
-    }
+        /**
+         * Gets the value of the viewreference property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isViewreference() {
+            return viewreference;
+        }
 
-    /**
-     * Sets the value of the zDim property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setZDim(Integer value)
-    {
-      this.zDim = value;
-    }
+        /**
+         * Sets the value of the viewreference property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setViewreference(Boolean value) {
+            this.viewreference = value;
+        }
 
-    /**
-     * Gets the value of the bgColour property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getBgColour()
-    {
-      return bgColour;
-    }
 
-    /**
-     * Sets the value of the bgColour property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setBgColour(Integer value)
-    {
-      this.bgColour = value;
-    }
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;extension base="{www.jalview.org}pdbentry">
+         *       &lt;sequence>
+         *         &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
+         *           &lt;complexType>
+         *             &lt;simpleContent>
+         *               &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
+         *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+         *                 &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *                 &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+         *                 &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+         *                 &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+         *                 &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *               &lt;/extension>
+         *             &lt;/simpleContent>
+         *           &lt;/complexType>
+         *         &lt;/element>
+         *       &lt;/sequence>
+         *     &lt;/extension>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "", propOrder = {
+            "structureState"
+        })
+        public static class Pdbids
+            extends Pdbentry
+        {
 
-    /**
-     * Gets the value of the scaleFactor property.
-     * 
-     * @return possible object is {@link Float }
-     * 
-     */
-    public Float getScaleFactor()
-    {
-      return scaleFactor;
-    }
+            @XmlElement(namespace = "www.jalview.org")
+            protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
+
+            /**
+             * Gets the value of the structureState property.
+             * 
+             * <p>
+             * This accessor method returns a reference to the live list,
+             * not a snapshot. Therefore any modification you make to the
+             * returned list will be present inside the JAXB object.
+             * This is why there is not a <CODE>set</CODE> method for the structureState property.
+             * 
+             * <p>
+             * For example, to add a new item, do as follows:
+             * <pre>
+             *    getStructureState().add(newItem);
+             * </pre>
+             * 
+             * 
+             * <p>
+             * Objects of the following type(s) are allowed in the list
+             * {@link JalviewModel.JSeq.Pdbids.StructureState }
+             * 
+             * 
+             */
+            public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
+                if (structureState == null) {
+                    structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
+                }
+                return this.structureState;
+            }
+
+
+            /**
+             * <p>Java class for anonymous complex type.
+             * 
+             * <p>The following schema fragment specifies the expected content contained within this class.
+             * 
+             * <pre>
+             * &lt;complexType>
+             *   &lt;simpleContent>
+             *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
+             *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+             *       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+             *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+             *       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+             *       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+             *       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *     &lt;/extension>
+             *   &lt;/simpleContent>
+             * &lt;/complexType>
+             * </pre>
+             * 
+             * 
+             */
+            @XmlAccessorType(XmlAccessType.FIELD)
+            @XmlType(name = "", propOrder = {
+                "value"
+            })
+            public static class StructureState {
+
+                @XmlValue
+                protected String value;
+                @XmlAttribute(name = "visible")
+                protected Boolean visible;
+                @XmlAttribute(name = "viewId")
+                protected String viewId;
+                @XmlAttribute(name = "alignwithAlignPanel")
+                protected Boolean alignwithAlignPanel;
+                @XmlAttribute(name = "colourwithAlignPanel")
+                protected Boolean colourwithAlignPanel;
+                @XmlAttribute(name = "colourByJmol")
+                protected Boolean colourByJmol;
+                @XmlAttribute(name = "type")
+                protected String type;
+                @XmlAttribute(name = "width")
+                protected Integer width;
+                @XmlAttribute(name = "height")
+                protected Integer height;
+                @XmlAttribute(name = "xpos")
+                protected Integer xpos;
+                @XmlAttribute(name = "ypos")
+                protected Integer ypos;
+
+                /**
+                 * Gets the value of the value property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link String }
+                 *     
+                 */
+                public String getValue() {
+                    return value;
+                }
+
+                /**
+                 * Sets the value of the value property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link String }
+                 *     
+                 */
+                public void setValue(String value) {
+                    this.value = value;
+                }
+
+                /**
+                 * Gets the value of the visible property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public Boolean isVisible() {
+                    return visible;
+                }
+
+                /**
+                 * Sets the value of the visible property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public void setVisible(Boolean value) {
+                    this.visible = value;
+                }
+
+                /**
+                 * Gets the value of the viewId property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link String }
+                 *     
+                 */
+                public String getViewId() {
+                    return viewId;
+                }
+
+                /**
+                 * Sets the value of the viewId property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link String }
+                 *     
+                 */
+                public void setViewId(String value) {
+                    this.viewId = value;
+                }
+
+                /**
+                 * Gets the value of the alignwithAlignPanel property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public boolean isAlignwithAlignPanel() {
+                    if (alignwithAlignPanel == null) {
+                        return true;
+                    } else {
+                        return alignwithAlignPanel;
+                    }
+                }
+
+                /**
+                 * Sets the value of the alignwithAlignPanel property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public void setAlignwithAlignPanel(Boolean value) {
+                    this.alignwithAlignPanel = value;
+                }
+
+                /**
+                 * Gets the value of the colourwithAlignPanel property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public boolean isColourwithAlignPanel() {
+                    if (colourwithAlignPanel == null) {
+                        return false;
+                    } else {
+                        return colourwithAlignPanel;
+                    }
+                }
+
+                /**
+                 * Sets the value of the colourwithAlignPanel property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public void setColourwithAlignPanel(Boolean value) {
+                    this.colourwithAlignPanel = value;
+                }
+
+                /**
+                 * Gets the value of the colourByJmol property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public boolean isColourByJmol() {
+                    if (colourByJmol == null) {
+                        return true;
+                    } else {
+                        return colourByJmol;
+                    }
+                }
+
+                /**
+                 * Sets the value of the colourByJmol property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public void setColourByJmol(Boolean value) {
+                    this.colourByJmol = value;
+                }
+
+                /**
+                 * Gets the value of the type property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link String }
+                 *     
+                 */
+                public String getType() {
+                    return type;
+                }
+
+                /**
+                 * Sets the value of the type property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link String }
+                 *     
+                 */
+                public void setType(String value) {
+                    this.type = value;
+                }
+
+                /**
+                 * Gets the value of the width property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Integer }
+                 *     
+                 */
+                public Integer getWidth() {
+                    return width;
+                }
+
+                /**
+                 * Sets the value of the width property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Integer }
+                 *     
+                 */
+                public void setWidth(Integer value) {
+                    this.width = value;
+                }
+
+                /**
+                 * Gets the value of the height property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Integer }
+                 *     
+                 */
+                public Integer getHeight() {
+                    return height;
+                }
+
+                /**
+                 * Sets the value of the height property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Integer }
+                 *     
+                 */
+                public void setHeight(Integer value) {
+                    this.height = value;
+                }
+
+                /**
+                 * Gets the value of the xpos property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Integer }
+                 *     
+                 */
+                public Integer getXpos() {
+                    return xpos;
+                }
+
+                /**
+                 * Sets the value of the xpos property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Integer }
+                 *     
+                 */
+                public void setXpos(Integer value) {
+                    this.xpos = value;
+                }
+
+                /**
+                 * Gets the value of the ypos property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Integer }
+                 *     
+                 */
+                public Integer getYpos() {
+                    return ypos;
+                }
+
+                /**
+                 * Sets the value of the ypos property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Integer }
+                 *     
+                 */
+                public void setYpos(Integer value) {
+                    this.ypos = value;
+                }
+
+            }
 
-    /**
-     * Sets the value of the scaleFactor property.
-     * 
-     * @param value
-     *          allowed object is {@link Float }
-     * 
-     */
-    public void setScaleFactor(Float value)
-    {
-      this.scaleFactor = value;
-    }
+        }
 
-    /**
-     * Gets the value of the showLabels property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowLabels()
-    {
-      return showLabels;
-    }
 
-    /**
-     * Sets the value of the showLabels property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowLabels(Boolean value)
-    {
-      this.showLabels = value;
-    }
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       &lt;sequence>
+         *         &lt;element name="secondaryStructure" maxOccurs="unbounded">
+         *           &lt;complexType>
+         *             &lt;complexContent>
+         *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *                 &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *                 &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *                 &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *               &lt;/restriction>
+         *             &lt;/complexContent>
+         *           &lt;/complexType>
+         *         &lt;/element>
+         *       &lt;/sequence>
+         *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+         *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *     &lt;/restriction>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "", propOrder = {
+            "secondaryStructure"
+        })
+        public static class RnaViewer {
+
+            @XmlElement(namespace = "www.jalview.org", required = true)
+            protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
+            @XmlAttribute(name = "title")
+            protected String title;
+            @XmlAttribute(name = "viewId")
+            protected String viewId;
+            @XmlAttribute(name = "dividerLocation")
+            protected Integer dividerLocation;
+            @XmlAttribute(name = "selectedRna")
+            protected Integer selectedRna;
+            @XmlAttribute(name = "width")
+            protected Integer width;
+            @XmlAttribute(name = "height")
+            protected Integer height;
+            @XmlAttribute(name = "xpos")
+            protected Integer xpos;
+            @XmlAttribute(name = "ypos")
+            protected Integer ypos;
+
+            /**
+             * Gets the value of the secondaryStructure property.
+             * 
+             * <p>
+             * This accessor method returns a reference to the live list,
+             * not a snapshot. Therefore any modification you make to the
+             * returned list will be present inside the JAXB object.
+             * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
+             * 
+             * <p>
+             * For example, to add a new item, do as follows:
+             * <pre>
+             *    getSecondaryStructure().add(newItem);
+             * </pre>
+             * 
+             * 
+             * <p>
+             * Objects of the following type(s) are allowed in the list
+             * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
+             * 
+             * 
+             */
+            public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
+                if (secondaryStructure == null) {
+                    secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
+                }
+                return this.secondaryStructure;
+            }
+
+            /**
+             * Gets the value of the title property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getTitle() {
+                return title;
+            }
+
+            /**
+             * Sets the value of the title property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setTitle(String value) {
+                this.title = value;
+            }
+
+            /**
+             * Gets the value of the viewId property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getViewId() {
+                return viewId;
+            }
+
+            /**
+             * Sets the value of the viewId property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setViewId(String value) {
+                this.viewId = value;
+            }
+
+            /**
+             * Gets the value of the dividerLocation property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getDividerLocation() {
+                return dividerLocation;
+            }
+
+            /**
+             * Sets the value of the dividerLocation property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setDividerLocation(Integer value) {
+                this.dividerLocation = value;
+            }
+
+            /**
+             * Gets the value of the selectedRna property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getSelectedRna() {
+                return selectedRna;
+            }
+
+            /**
+             * Sets the value of the selectedRna property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setSelectedRna(Integer value) {
+                this.selectedRna = value;
+            }
+
+            /**
+             * Gets the value of the width property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getWidth() {
+                return width;
+            }
+
+            /**
+             * Sets the value of the width property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setWidth(Integer value) {
+                this.width = value;
+            }
+
+            /**
+             * Gets the value of the height property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getHeight() {
+                return height;
+            }
+
+            /**
+             * Sets the value of the height property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setHeight(Integer value) {
+                this.height = value;
+            }
+
+            /**
+             * Gets the value of the xpos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getXpos() {
+                return xpos;
+            }
+
+            /**
+             * Sets the value of the xpos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setXpos(Integer value) {
+                this.xpos = value;
+            }
+
+            /**
+             * Gets the value of the ypos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getYpos() {
+                return ypos;
+            }
+
+            /**
+             * Sets the value of the ypos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setYpos(Integer value) {
+                this.ypos = value;
+            }
+
+
+            /**
+             * <p>Java class for anonymous complex type.
+             * 
+             * <p>The following schema fragment specifies the expected content contained within this class.
+             * 
+             * <pre>
+             * &lt;complexType>
+             *   &lt;complexContent>
+             *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+             *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+             *       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *     &lt;/restriction>
+             *   &lt;/complexContent>
+             * &lt;/complexType>
+             * </pre>
+             * 
+             * 
+             */
+            @XmlAccessorType(XmlAccessType.FIELD)
+            @XmlType(name = "")
+            public static class SecondaryStructure {
+
+                @XmlAttribute(name = "title")
+                protected String title;
+                @XmlAttribute(name = "annotationId", required = true)
+                protected String annotationId;
+                @XmlAttribute(name = "gapped")
+                protected Boolean gapped;
+                @XmlAttribute(name = "viewerState")
+                protected String viewerState;
+
+                /**
+                 * Gets the value of the title property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link String }
+                 *     
+                 */
+                public String getTitle() {
+                    return title;
+                }
+
+                /**
+                 * Sets the value of the title property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link String }
+                 *     
+                 */
+                public void setTitle(String value) {
+                    this.title = value;
+                }
+
+                /**
+                 * Gets the value of the annotationId property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link String }
+                 *     
+                 */
+                public String getAnnotationId() {
+                    return annotationId;
+                }
+
+                /**
+                 * Sets the value of the annotationId property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link String }
+                 *     
+                 */
+                public void setAnnotationId(String value) {
+                    this.annotationId = value;
+                }
+
+                /**
+                 * Gets the value of the gapped property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public Boolean isGapped() {
+                    return gapped;
+                }
+
+                /**
+                 * Sets the value of the gapped property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public void setGapped(Boolean value) {
+                    this.gapped = value;
+                }
+
+                /**
+                 * Gets the value of the viewerState property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link String }
+                 *     
+                 */
+                public String getViewerState() {
+                    return viewerState;
+                }
+
+                /**
+                 * Sets the value of the viewerState property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link String }
+                 *     
+                 */
+                public void setViewerState(String value) {
+                    this.viewerState = value;
+                }
+
+            }
 
-    /**
-     * Gets the value of the linkToAllViews property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isLinkToAllViews()
-    {
-      return linkToAllViews;
-    }
+        }
 
-    /**
-     * Sets the value of the linkToAllViews property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setLinkToAllViews(Boolean value)
-    {
-      this.linkToAllViews = value;
     }
 
-    /**
-     * Gets the value of the width property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getWidth()
-    {
-      return width;
-    }
 
     /**
-     * Sets the value of the width property.
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="sequencePoint" maxOccurs="unbounded">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 &lt;attGroup ref="{www.jalview.org}position"/>
+     *                 &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *               &lt;/restriction>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *         &lt;element name="axis" maxOccurs="3" minOccurs="3">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 &lt;attGroup ref="{www.jalview.org}position"/>
+     *               &lt;/restriction>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *         &lt;element name="seqPointMin">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 &lt;attGroup ref="{www.jalview.org}position"/>
+     *               &lt;/restriction>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *         &lt;element name="seqPointMax">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 &lt;attGroup ref="{www.jalview.org}position"/>
+     *               &lt;/restriction>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *         &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
+     *       &lt;/sequence>
+     *       &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
+     *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+     *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
      * 
-     * @param value
-     *          allowed object is {@link Integer }
      * 
      */
-    public void setWidth(Integer value)
-    {
-      this.width = value;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "sequencePoint",
+        "axis",
+        "seqPointMin",
+        "seqPointMax",
+        "pcaData"
+    })
+    public static class PcaViewer {
+
+        @XmlElement(namespace = "www.jalview.org", required = true)
+        protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
+        @XmlElement(namespace = "www.jalview.org", required = true)
+        protected List<JalviewModel.PcaViewer.Axis> axis;
+        @XmlElement(namespace = "www.jalview.org", required = true)
+        protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
+        @XmlElement(namespace = "www.jalview.org", required = true)
+        protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
+        @XmlElement(namespace = "www.jalview.org", required = true)
+        protected PcaDataType pcaData;
+        @XmlAttribute(name = "title")
+        protected String title;
+        @XmlAttribute(name = "scoreModelName")
+        protected String scoreModelName;
+        @XmlAttribute(name = "xDim")
+        protected Integer xDim;
+        @XmlAttribute(name = "yDim")
+        protected Integer yDim;
+        @XmlAttribute(name = "zDim")
+        protected Integer zDim;
+        @XmlAttribute(name = "bgColour")
+        protected Integer bgColour;
+        @XmlAttribute(name = "scaleFactor")
+        protected Float scaleFactor;
+        @XmlAttribute(name = "showLabels")
+        protected Boolean showLabels;
+        @XmlAttribute(name = "linkToAllViews")
+        protected Boolean linkToAllViews;
+        @XmlAttribute(name = "includeGaps")
+        protected Boolean includeGaps;
+        @XmlAttribute(name = "matchGaps")
+        protected Boolean matchGaps;
+        @XmlAttribute(name = "includeGappedColumns")
+        protected Boolean includeGappedColumns;
+        @XmlAttribute(name = "denominateByShortestLength")
+        protected Boolean denominateByShortestLength;
+        @XmlAttribute(name = "width")
+        protected Integer width;
+        @XmlAttribute(name = "height")
+        protected Integer height;
+        @XmlAttribute(name = "xpos")
+        protected Integer xpos;
+        @XmlAttribute(name = "ypos")
+        protected Integer ypos;
 
-    /**
-     * Gets the value of the height property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getHeight()
-    {
-      return height;
-    }
+        /**
+         * Gets the value of the sequencePoint property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getSequencePoint().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.PcaViewer.SequencePoint }
+         * 
+         * 
+         */
+        public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
+            if (sequencePoint == null) {
+                sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
+            }
+            return this.sequencePoint;
+        }
 
-    /**
-     * Sets the value of the height property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setHeight(Integer value)
-    {
-      this.height = value;
-    }
+        /**
+         * Gets the value of the axis property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the axis property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getAxis().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.PcaViewer.Axis }
+         * 
+         * 
+         */
+        public List<JalviewModel.PcaViewer.Axis> getAxis() {
+            if (axis == null) {
+                axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
+            }
+            return this.axis;
+        }
 
-    /**
-     * Gets the value of the xpos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getXpos()
-    {
-      return xpos;
-    }
+        /**
+         * Gets the value of the seqPointMin property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link JalviewModel.PcaViewer.SeqPointMin }
+         *     
+         */
+        public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
+            return seqPointMin;
+        }
 
-    /**
-     * Sets the value of the xpos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setXpos(Integer value)
-    {
-      this.xpos = value;
-    }
+        /**
+         * Sets the value of the seqPointMin property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link JalviewModel.PcaViewer.SeqPointMin }
+         *     
+         */
+        public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
+            this.seqPointMin = value;
+        }
 
-    /**
-     * Gets the value of the ypos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getYpos()
-    {
-      return ypos;
-    }
+        /**
+         * Gets the value of the seqPointMax property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link JalviewModel.PcaViewer.SeqPointMax }
+         *     
+         */
+        public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
+            return seqPointMax;
+        }
 
-    /**
-     * Sets the value of the ypos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setYpos(Integer value)
-    {
-      this.ypos = value;
-    }
+        /**
+         * Sets the value of the seqPointMax property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link JalviewModel.PcaViewer.SeqPointMax }
+         *     
+         */
+        public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
+            this.seqPointMax = value;
+        }
 
-    /**
-     * Gets the value of the includeGaps property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isIncludeGaps()
-    {
-      return includeGaps;
-    }
+        /**
+         * Gets the value of the pcaData property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link PcaDataType }
+         *     
+         */
+        public PcaDataType getPcaData() {
+            return pcaData;
+        }
 
-    /**
-     * Sets the value of the includeGaps property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setIncludeGaps(Boolean value)
-    {
-      this.includeGaps = value;
-    }
+        /**
+         * Sets the value of the pcaData property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link PcaDataType }
+         *     
+         */
+        public void setPcaData(PcaDataType value) {
+            this.pcaData = value;
+        }
 
-    /**
-     * Gets the value of the matchGaps property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isMatchGaps()
-    {
-      return matchGaps;
-    }
+        /**
+         * Gets the value of the title property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getTitle() {
+            return title;
+        }
 
-    /**
-     * Sets the value of the matchGaps property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setMatchGaps(Boolean value)
-    {
-      this.matchGaps = value;
-    }
+        /**
+         * Sets the value of the title property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setTitle(String value) {
+            this.title = value;
+        }
 
-    /**
-     * Gets the value of the includeGappedColumns property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isIncludeGappedColumns()
-    {
-      return includeGappedColumns;
-    }
+        /**
+         * Gets the value of the scoreModelName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getScoreModelName() {
+            return scoreModelName;
+        }
 
-    /**
-     * Sets the value of the includeGappedColumns property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setIncludeGappedColumns(Boolean value)
-    {
-      this.includeGappedColumns = value;
-    }
+        /**
+         * Sets the value of the scoreModelName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setScoreModelName(String value) {
+            this.scoreModelName = value;
+        }
 
-    /**
-     * Gets the value of the denominateByShortestLength property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isDenominateByShortestLength()
-    {
-      return denominateByShortestLength;
-    }
+        /**
+         * Gets the value of the xDim property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getXDim() {
+            return xDim;
+        }
 
-    /**
-     * Sets the value of the denominateByShortestLength property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setDenominateByShortestLength(Boolean value)
-    {
-      this.denominateByShortestLength = value;
-    }
+        /**
+         * Sets the value of the xDim property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setXDim(Integer value) {
+            this.xDim = value;
+        }
 
-    /**
-     * &lt;p&gt;Java class for anonymous complex type.
-     * 
-     * &lt;p&gt;The following schema fragment specifies the expected content
-     * contained within this class.
-     * 
-     * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-     * &amp;lt;restriction
-     * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
-     * ref="{www.jalview.org}position"/&amp;gt; &amp;lt;/restriction&amp;gt;
-     * &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class Axis
-    {
-
-      @XmlAttribute(name = "xPos")
-      protected Float xPos;
-
-      @XmlAttribute(name = "yPos")
-      protected Float yPos;
-
-      @XmlAttribute(name = "zPos")
-      protected Float zPos;
-
-      /**
-       * Gets the value of the xPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getXPos()
-      {
-        return xPos;
-      }
-
-      /**
-       * Sets the value of the xPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setXPos(Float value)
-      {
-        this.xPos = value;
-      }
-
-      /**
-       * Gets the value of the yPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getYPos()
-      {
-        return yPos;
-      }
-
-      /**
-       * Sets the value of the yPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setYPos(Float value)
-      {
-        this.yPos = value;
-      }
-
-      /**
-       * Gets the value of the zPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getZPos()
-      {
-        return zPos;
-      }
-
-      /**
-       * Sets the value of the zPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setZPos(Float value)
-      {
-        this.zPos = value;
-      }
+        /**
+         * Gets the value of the yDim property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getYDim() {
+            return yDim;
+        }
 
-    }
+        /**
+         * Sets the value of the yDim property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setYDim(Integer value) {
+            this.yDim = value;
+        }
 
-    /**
-     * &lt;p&gt;Java class for anonymous complex type.
-     * 
-     * &lt;p&gt;The following schema fragment specifies the expected content
-     * contained within this class.
-     * 
-     * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-     * &amp;lt;restriction
-     * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
-     * ref="{www.jalview.org}position"/&amp;gt; &amp;lt;/restriction&amp;gt;
-     * &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class SeqPointMax
-    {
-
-      @XmlAttribute(name = "xPos")
-      protected Float xPos;
-
-      @XmlAttribute(name = "yPos")
-      protected Float yPos;
-
-      @XmlAttribute(name = "zPos")
-      protected Float zPos;
-
-      /**
-       * Gets the value of the xPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getXPos()
-      {
-        return xPos;
-      }
-
-      /**
-       * Sets the value of the xPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setXPos(Float value)
-      {
-        this.xPos = value;
-      }
-
-      /**
-       * Gets the value of the yPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getYPos()
-      {
-        return yPos;
-      }
-
-      /**
-       * Sets the value of the yPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setYPos(Float value)
-      {
-        this.yPos = value;
-      }
-
-      /**
-       * Gets the value of the zPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getZPos()
-      {
-        return zPos;
-      }
-
-      /**
-       * Sets the value of the zPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setZPos(Float value)
-      {
-        this.zPos = value;
-      }
+        /**
+         * Gets the value of the zDim property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getZDim() {
+            return zDim;
+        }
 
-    }
+        /**
+         * Sets the value of the zDim property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setZDim(Integer value) {
+            this.zDim = value;
+        }
 
-    /**
-     * &lt;p&gt;Java class for anonymous complex type.
-     * 
-     * &lt;p&gt;The following schema fragment specifies the expected content
-     * contained within this class.
-     * 
-     * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-     * &amp;lt;restriction
-     * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
-     * ref="{www.jalview.org}position"/&amp;gt; &amp;lt;/restriction&amp;gt;
-     * &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class SeqPointMin
-    {
-
-      @XmlAttribute(name = "xPos")
-      protected Float xPos;
-
-      @XmlAttribute(name = "yPos")
-      protected Float yPos;
-
-      @XmlAttribute(name = "zPos")
-      protected Float zPos;
-
-      /**
-       * Gets the value of the xPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getXPos()
-      {
-        return xPos;
-      }
-
-      /**
-       * Sets the value of the xPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setXPos(Float value)
-      {
-        this.xPos = value;
-      }
-
-      /**
-       * Gets the value of the yPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getYPos()
-      {
-        return yPos;
-      }
-
-      /**
-       * Sets the value of the yPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setYPos(Float value)
-      {
-        this.yPos = value;
-      }
-
-      /**
-       * Gets the value of the zPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getZPos()
-      {
-        return zPos;
-      }
-
-      /**
-       * Sets the value of the zPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setZPos(Float value)
-      {
-        this.zPos = value;
-      }
+        /**
+         * Gets the value of the bgColour property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getBgColour() {
+            return bgColour;
+        }
 
-    }
+        /**
+         * Sets the value of the bgColour property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setBgColour(Integer value) {
+            this.bgColour = value;
+        }
 
-    /**
-     * &lt;p&gt;Java class for anonymous complex type.
-     * 
-     * &lt;p&gt;The following schema fragment specifies the expected content
-     * contained within this class.
-     * 
-     * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-     * &amp;lt;restriction
-     * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
-     * ref="{www.jalview.org}position"/&amp;gt; &amp;lt;attribute
-     * name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string"
-     * /&amp;gt; &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-     * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class SequencePoint
-    {
-
-      @XmlAttribute(name = "sequenceRef")
-      protected String sequenceRef;
-
-      @XmlAttribute(name = "xPos")
-      protected Float xPos;
-
-      @XmlAttribute(name = "yPos")
-      protected Float yPos;
-
-      @XmlAttribute(name = "zPos")
-      protected Float zPos;
-
-      /**
-       * Gets the value of the sequenceRef property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getSequenceRef()
-      {
-        return sequenceRef;
-      }
-
-      /**
-       * Sets the value of the sequenceRef property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setSequenceRef(String value)
-      {
-        this.sequenceRef = value;
-      }
-
-      /**
-       * Gets the value of the xPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getXPos()
-      {
-        return xPos;
-      }
-
-      /**
-       * Sets the value of the xPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setXPos(Float value)
-      {
-        this.xPos = value;
-      }
-
-      /**
-       * Gets the value of the yPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getYPos()
-      {
-        return yPos;
-      }
-
-      /**
-       * Sets the value of the yPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setYPos(Float value)
-      {
-        this.yPos = value;
-      }
-
-      /**
-       * Gets the value of the zPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getZPos()
-      {
-        return zPos;
-      }
-
-      /**
-       * Sets the value of the zPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setZPos(Float value)
-      {
-        this.zPos = value;
-      }
+        /**
+         * Gets the value of the scaleFactor property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Float }
+         *     
+         */
+        public Float getScaleFactor() {
+            return scaleFactor;
+        }
 
-    }
+        /**
+         * Sets the value of the scaleFactor property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Float }
+         *     
+         */
+        public void setScaleFactor(Float value) {
+            this.scaleFactor = value;
+        }
 
-  }
-
-  /**
-   * &lt;p&gt;Java class for anonymous complex type.
-   * 
-   * &lt;p&gt;The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-   * &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;sequence
-   * minOccurs="0"&amp;gt; &amp;lt;element name="title"
-   * type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt; &amp;lt;element
-   * name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
-   * &amp;lt;/sequence&amp;gt; &amp;lt;attGroup
-   * ref="{www.jalview.org}swingwindow"/&amp;gt; &amp;lt;attribute
-   * name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-   * &amp;lt;attribute name="fontSize"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
-   * name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
-   * &amp;lt;attribute name="threshold"
-   * type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt; &amp;lt;attribute
-   * name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean"
-   * /&amp;gt; &amp;lt;attribute name="showDistances"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;attribute name="markUnlinked"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;attribute name="fitToWindow"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;attribute name="currentTree"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID"
-   * /&amp;gt; &amp;lt;attribute name="linkToAllViews"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
-   * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "title", "newick" })
-  public static class Tree
-  {
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected String title;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected String newick;
-
-    @XmlAttribute(name = "fontName")
-    protected String fontName;
-
-    @XmlAttribute(name = "fontSize")
-    protected Integer fontSize;
-
-    @XmlAttribute(name = "fontStyle")
-    protected Integer fontStyle;
-
-    @XmlAttribute(name = "threshold")
-    protected Float threshold;
-
-    @XmlAttribute(name = "showBootstrap")
-    protected Boolean showBootstrap;
-
-    @XmlAttribute(name = "showDistances")
-    protected Boolean showDistances;
-
-    @XmlAttribute(name = "markUnlinked")
-    protected Boolean markUnlinked;
-
-    @XmlAttribute(name = "fitToWindow")
-    protected Boolean fitToWindow;
-
-    @XmlAttribute(name = "currentTree")
-    protected Boolean currentTree;
-
-    @XmlAttribute(name = "id")
-    @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
-    @XmlID
-    @XmlSchemaType(name = "ID")
-    protected String id;
-
-    @XmlAttribute(name = "linkToAllViews")
-    protected Boolean linkToAllViews;
-
-    @XmlAttribute(name = "width")
-    protected Integer width;
-
-    @XmlAttribute(name = "height")
-    protected Integer height;
-
-    @XmlAttribute(name = "xpos")
-    protected Integer xpos;
-
-    @XmlAttribute(name = "ypos")
-    protected Integer ypos;
+        /**
+         * Gets the value of the showLabels property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowLabels() {
+            return showLabels;
+        }
 
-    /**
-     * Gets the value of the title property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getTitle()
-    {
-      return title;
-    }
+        /**
+         * Sets the value of the showLabels property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowLabels(Boolean value) {
+            this.showLabels = value;
+        }
 
-    /**
-     * Sets the value of the title property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setTitle(String value)
-    {
-      this.title = value;
-    }
+        /**
+         * Gets the value of the linkToAllViews property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isLinkToAllViews() {
+            return linkToAllViews;
+        }
 
-    /**
-     * Gets the value of the newick property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getNewick()
-    {
-      return newick;
-    }
+        /**
+         * Sets the value of the linkToAllViews property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setLinkToAllViews(Boolean value) {
+            this.linkToAllViews = value;
+        }
 
-    /**
-     * Sets the value of the newick property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setNewick(String value)
-    {
-      this.newick = value;
-    }
+        /**
+         * Gets the value of the includeGaps property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isIncludeGaps() {
+            return includeGaps;
+        }
 
-    /**
-     * Gets the value of the fontName property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getFontName()
-    {
-      return fontName;
-    }
+        /**
+         * Sets the value of the includeGaps property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setIncludeGaps(Boolean value) {
+            this.includeGaps = value;
+        }
 
-    /**
-     * Sets the value of the fontName property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setFontName(String value)
-    {
-      this.fontName = value;
-    }
+        /**
+         * Gets the value of the matchGaps property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isMatchGaps() {
+            return matchGaps;
+        }
 
-    /**
-     * Gets the value of the fontSize property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getFontSize()
-    {
-      return fontSize;
-    }
+        /**
+         * Sets the value of the matchGaps property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setMatchGaps(Boolean value) {
+            this.matchGaps = value;
+        }
 
-    /**
-     * Sets the value of the fontSize property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setFontSize(Integer value)
-    {
-      this.fontSize = value;
-    }
+        /**
+         * Gets the value of the includeGappedColumns property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isIncludeGappedColumns() {
+            return includeGappedColumns;
+        }
 
-    /**
-     * Gets the value of the fontStyle property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getFontStyle()
-    {
-      return fontStyle;
-    }
+        /**
+         * Sets the value of the includeGappedColumns property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setIncludeGappedColumns(Boolean value) {
+            this.includeGappedColumns = value;
+        }
 
-    /**
-     * Sets the value of the fontStyle property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setFontStyle(Integer value)
-    {
-      this.fontStyle = value;
-    }
+        /**
+         * Gets the value of the denominateByShortestLength property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isDenominateByShortestLength() {
+            return denominateByShortestLength;
+        }
 
-    /**
-     * Gets the value of the threshold property.
-     * 
-     * @return possible object is {@link Float }
-     * 
-     */
-    public Float getThreshold()
-    {
-      return threshold;
-    }
+        /**
+         * Sets the value of the denominateByShortestLength property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setDenominateByShortestLength(Boolean value) {
+            this.denominateByShortestLength = value;
+        }
 
-    /**
-     * Sets the value of the threshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Float }
-     * 
-     */
-    public void setThreshold(Float value)
-    {
-      this.threshold = value;
-    }
+        /**
+         * Gets the value of the width property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getWidth() {
+            return width;
+        }
 
-    /**
-     * Gets the value of the showBootstrap property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowBootstrap()
-    {
-      return showBootstrap;
-    }
+        /**
+         * Sets the value of the width property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setWidth(Integer value) {
+            this.width = value;
+        }
 
-    /**
-     * Sets the value of the showBootstrap property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowBootstrap(Boolean value)
-    {
-      this.showBootstrap = value;
-    }
+        /**
+         * Gets the value of the height property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getHeight() {
+            return height;
+        }
 
-    /**
-     * Gets the value of the showDistances property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowDistances()
-    {
-      return showDistances;
-    }
+        /**
+         * Sets the value of the height property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setHeight(Integer value) {
+            this.height = value;
+        }
 
-    /**
-     * Sets the value of the showDistances property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowDistances(Boolean value)
-    {
-      this.showDistances = value;
-    }
+        /**
+         * Gets the value of the xpos property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getXpos() {
+            return xpos;
+        }
 
-    /**
-     * Gets the value of the markUnlinked property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isMarkUnlinked()
-    {
-      return markUnlinked;
-    }
+        /**
+         * Sets the value of the xpos property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setXpos(Integer value) {
+            this.xpos = value;
+        }
 
-    /**
-     * Sets the value of the markUnlinked property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setMarkUnlinked(Boolean value)
-    {
-      this.markUnlinked = value;
-    }
+        /**
+         * Gets the value of the ypos property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getYpos() {
+            return ypos;
+        }
 
-    /**
-     * Gets the value of the fitToWindow property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isFitToWindow()
-    {
-      return fitToWindow;
-    }
+        /**
+         * Sets the value of the ypos property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setYpos(Integer value) {
+            this.ypos = value;
+        }
 
-    /**
-     * Sets the value of the fitToWindow property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setFitToWindow(Boolean value)
-    {
-      this.fitToWindow = value;
-    }
 
-    /**
-     * Gets the value of the currentTree property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isCurrentTree()
-    {
-      return currentTree;
-    }
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       &lt;attGroup ref="{www.jalview.org}position"/>
+         *     &lt;/restriction>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class Axis {
+
+            @XmlAttribute(name = "xPos")
+            protected Float xPos;
+            @XmlAttribute(name = "yPos")
+            protected Float yPos;
+            @XmlAttribute(name = "zPos")
+            protected Float zPos;
+
+            /**
+             * Gets the value of the xPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getXPos() {
+                return xPos;
+            }
+
+            /**
+             * Sets the value of the xPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setXPos(Float value) {
+                this.xPos = value;
+            }
+
+            /**
+             * Gets the value of the yPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getYPos() {
+                return yPos;
+            }
+
+            /**
+             * Sets the value of the yPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setYPos(Float value) {
+                this.yPos = value;
+            }
+
+            /**
+             * Gets the value of the zPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getZPos() {
+                return zPos;
+            }
+
+            /**
+             * Sets the value of the zPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setZPos(Float value) {
+                this.zPos = value;
+            }
 
-    /**
-     * Sets the value of the currentTree property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setCurrentTree(Boolean value)
-    {
-      this.currentTree = value;
-    }
+        }
 
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getId()
-    {
-      return id;
-    }
 
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setId(String value)
-    {
-      this.id = value;
-    }
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       &lt;attGroup ref="{www.jalview.org}position"/>
+         *     &lt;/restriction>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class SeqPointMax {
+
+            @XmlAttribute(name = "xPos")
+            protected Float xPos;
+            @XmlAttribute(name = "yPos")
+            protected Float yPos;
+            @XmlAttribute(name = "zPos")
+            protected Float zPos;
+
+            /**
+             * Gets the value of the xPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getXPos() {
+                return xPos;
+            }
+
+            /**
+             * Sets the value of the xPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setXPos(Float value) {
+                this.xPos = value;
+            }
+
+            /**
+             * Gets the value of the yPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getYPos() {
+                return yPos;
+            }
+
+            /**
+             * Sets the value of the yPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setYPos(Float value) {
+                this.yPos = value;
+            }
+
+            /**
+             * Gets the value of the zPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getZPos() {
+                return zPos;
+            }
+
+            /**
+             * Sets the value of the zPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setZPos(Float value) {
+                this.zPos = value;
+            }
 
-    /**
-     * Gets the value of the linkToAllViews property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isLinkToAllViews()
-    {
-      if (linkToAllViews == null)
-      {
-        return false;
-      }
-      else
-      {
-        return linkToAllViews;
-      }
-    }
+        }
+
+
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       &lt;attGroup ref="{www.jalview.org}position"/>
+         *     &lt;/restriction>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class SeqPointMin {
+
+            @XmlAttribute(name = "xPos")
+            protected Float xPos;
+            @XmlAttribute(name = "yPos")
+            protected Float yPos;
+            @XmlAttribute(name = "zPos")
+            protected Float zPos;
+
+            /**
+             * Gets the value of the xPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getXPos() {
+                return xPos;
+            }
+
+            /**
+             * Sets the value of the xPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setXPos(Float value) {
+                this.xPos = value;
+            }
+
+            /**
+             * Gets the value of the yPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getYPos() {
+                return yPos;
+            }
+
+            /**
+             * Sets the value of the yPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setYPos(Float value) {
+                this.yPos = value;
+            }
+
+            /**
+             * Gets the value of the zPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getZPos() {
+                return zPos;
+            }
+
+            /**
+             * Sets the value of the zPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setZPos(Float value) {
+                this.zPos = value;
+            }
+
+        }
+
+
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       &lt;attGroup ref="{www.jalview.org}position"/>
+         *       &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *     &lt;/restriction>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class SequencePoint {
+
+            @XmlAttribute(name = "sequenceRef")
+            protected String sequenceRef;
+            @XmlAttribute(name = "xPos")
+            protected Float xPos;
+            @XmlAttribute(name = "yPos")
+            protected Float yPos;
+            @XmlAttribute(name = "zPos")
+            protected Float zPos;
+
+            /**
+             * Gets the value of the sequenceRef property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getSequenceRef() {
+                return sequenceRef;
+            }
+
+            /**
+             * Sets the value of the sequenceRef property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setSequenceRef(String value) {
+                this.sequenceRef = value;
+            }
+
+            /**
+             * Gets the value of the xPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getXPos() {
+                return xPos;
+            }
+
+            /**
+             * Sets the value of the xPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setXPos(Float value) {
+                this.xPos = value;
+            }
+
+            /**
+             * Gets the value of the yPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getYPos() {
+                return yPos;
+            }
+
+            /**
+             * Sets the value of the yPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setYPos(Float value) {
+                this.yPos = value;
+            }
+
+            /**
+             * Gets the value of the zPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getZPos() {
+                return zPos;
+            }
+
+            /**
+             * Sets the value of the zPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setZPos(Float value) {
+                this.zPos = value;
+            }
+
+        }
 
-    /**
-     * Sets the value of the linkToAllViews property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setLinkToAllViews(Boolean value)
-    {
-      this.linkToAllViews = value;
     }
 
+
     /**
-     * Gets the value of the width property.
+     * <p>Java class for anonymous complex type.
      * 
-     * @return possible object is {@link Integer }
+     * <p>The following schema fragment specifies the expected content contained within this class.
      * 
-     */
-    public Integer getWidth()
-    {
-      return width;
-    }
-
-    /**
-     * Sets the value of the width property.
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence minOccurs="0">
+     *         &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+     *         &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+     *       &lt;/sequence>
+     *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+     *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+     *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
      * 
-     * @param value
-     *          allowed object is {@link Integer }
      * 
      */
-    public void setWidth(Integer value)
-    {
-      this.width = value;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "title",
+        "newick"
+    })
+    public static class Tree {
 
-    /**
-     * Gets the value of the height property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getHeight()
-    {
-      return height;
-    }
+        @XmlElement(namespace = "www.jalview.org")
+        protected String title;
+        @XmlElement(namespace = "www.jalview.org")
+        protected String newick;
+        @XmlAttribute(name = "fontName")
+        protected String fontName;
+        @XmlAttribute(name = "fontSize")
+        protected Integer fontSize;
+        @XmlAttribute(name = "fontStyle")
+        protected Integer fontStyle;
+        @XmlAttribute(name = "threshold")
+        protected Float threshold;
+        @XmlAttribute(name = "showBootstrap")
+        protected Boolean showBootstrap;
+        @XmlAttribute(name = "showDistances")
+        protected Boolean showDistances;
+        @XmlAttribute(name = "markUnlinked")
+        protected Boolean markUnlinked;
+        @XmlAttribute(name = "fitToWindow")
+        protected Boolean fitToWindow;
+        @XmlAttribute(name = "currentTree")
+        protected Boolean currentTree;
+        @XmlAttribute(name = "id")
+        @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+        @XmlID
+        @XmlSchemaType(name = "ID")
+        protected String id;
+        @XmlAttribute(name = "linkToAllViews")
+        protected Boolean linkToAllViews;
+        @XmlAttribute(name = "width")
+        protected Integer width;
+        @XmlAttribute(name = "height")
+        protected Integer height;
+        @XmlAttribute(name = "xpos")
+        protected Integer xpos;
+        @XmlAttribute(name = "ypos")
+        protected Integer ypos;
 
-    /**
-     * Sets the value of the height property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setHeight(Integer value)
-    {
-      this.height = value;
-    }
+        /**
+         * Gets the value of the title property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getTitle() {
+            return title;
+        }
 
-    /**
-     * Gets the value of the xpos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getXpos()
-    {
-      return xpos;
-    }
+        /**
+         * Sets the value of the title property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setTitle(String value) {
+            this.title = value;
+        }
 
-    /**
-     * Sets the value of the xpos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setXpos(Integer value)
-    {
-      this.xpos = value;
-    }
+        /**
+         * Gets the value of the newick property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getNewick() {
+            return newick;
+        }
 
-    /**
-     * Gets the value of the ypos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getYpos()
-    {
-      return ypos;
-    }
+        /**
+         * Sets the value of the newick property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setNewick(String value) {
+            this.newick = value;
+        }
 
-    /**
-     * Sets the value of the ypos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setYpos(Integer value)
-    {
-      this.ypos = value;
-    }
+        /**
+         * Gets the value of the fontName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getFontName() {
+            return fontName;
+        }
 
-  }
-
-  /**
-   * &lt;p&gt;Java class for anonymous complex type.
-   * 
-   * &lt;p&gt;The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-   * &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
-   * &amp;lt;sequence&amp;gt; &amp;lt;element name="UserColourScheme"
-   * type="{www.jalview.org/colours}JalviewUserColours"/&amp;gt;
-   * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="id"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-   * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "userColourScheme" })
-  public static class UserColours
-  {
-
-    @XmlElement(
-      name = "UserColourScheme",
-      namespace = "www.jalview.org",
-      required = true)
-    protected JalviewUserColours userColourScheme;
-
-    @XmlAttribute(name = "id")
-    protected String id;
+        /**
+         * Sets the value of the fontName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setFontName(String value) {
+            this.fontName = value;
+        }
 
-    /**
-     * Gets the value of the userColourScheme property.
-     * 
-     * @return possible object is {@link JalviewUserColours }
-     * 
-     */
-    public JalviewUserColours getUserColourScheme()
-    {
-      return userColourScheme;
-    }
+        /**
+         * Gets the value of the fontSize property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getFontSize() {
+            return fontSize;
+        }
 
-    /**
-     * Sets the value of the userColourScheme property.
-     * 
-     * @param value
-     *          allowed object is {@link JalviewUserColours }
-     * 
-     */
-    public void setUserColourScheme(JalviewUserColours value)
-    {
-      this.userColourScheme = value;
-    }
+        /**
+         * Sets the value of the fontSize property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setFontSize(Integer value) {
+            this.fontSize = value;
+        }
 
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getId()
-    {
-      return id;
-    }
+        /**
+         * Gets the value of the fontStyle property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getFontStyle() {
+            return fontStyle;
+        }
 
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setId(String value)
-    {
-      this.id = value;
-    }
+        /**
+         * Sets the value of the fontStyle property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setFontStyle(Integer value) {
+            this.fontStyle = value;
+        }
 
-  }
-
-  /**
-   * &lt;p&gt;Java class for anonymous complex type.
-   * 
-   * &lt;p&gt;The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-   * &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
-   * &amp;lt;sequence&amp;gt; &amp;lt;element name="AnnotationColours"
-   * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&amp;gt;
-   * &amp;lt;element name="hiddenColumns" maxOccurs="unbounded"
-   * minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
-   * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
-   * name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
-   * &amp;lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int"
-   * /&amp;gt; &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
-   * name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&amp;gt;
-   * &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-   * &amp;lt;extension
-   * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&amp;gt;
-   * &amp;lt;attribute name="calcId" use="required"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
-   * name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean"
-   * default="false" /&amp;gt; &amp;lt;attribute name="autoUpdate"
-   * use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;/extension&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
-   * &amp;lt;/sequence&amp;gt; &amp;lt;attGroup
-   * ref="{www.jalview.org}swingwindow"/&amp;gt; &amp;lt;attribute
-   * name="conservationSelected"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;attribute name="pidSelected"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;attribute name="bgColour"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
-   * name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
-   * &amp;lt;attribute name="pidThreshold"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
-   * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-   * &amp;lt;attribute name="showFullId"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;attribute name="rightAlignIds"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;attribute name="showText"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;attribute name="showColourText"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;attribute name="showUnconserved"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
-   * &amp;lt;attribute name="showBoxes"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;attribute name="wrapAlignment"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;attribute name="renderGaps"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;attribute name="showSequenceFeatures"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;attribute name="showNPfeatureTooltip"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;attribute name="showDbRefTooltip"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;attribute name="followHighlight"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
-   * &amp;lt;attribute name="followSelection"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
-   * &amp;lt;attribute name="showAnnotation"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;attribute name="centreColumnLabels"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
-   * &amp;lt;attribute name="showGroupConservation"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
-   * &amp;lt;attribute name="showGroupConsensus"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
-   * &amp;lt;attribute name="showConsensusHistogram"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
-   * &amp;lt;attribute name="showSequenceLogo"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
-   * &amp;lt;attribute name="normaliseSequenceLogo"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
-   * &amp;lt;attribute name="ignoreGapsinConsensus"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
-   * &amp;lt;attribute name="startRes"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
-   * name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
-   * &amp;lt;attribute name="fontName"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
-   * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
-   * &amp;lt;attribute name="fontStyle"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
-   * name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean"
-   * default="true" /&amp;gt; &amp;lt;attribute name="viewName"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
-   * name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string"
-   * /&amp;gt; &amp;lt;attribute name="gatheredViews"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;attribute name="textCol1"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
-   * name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
-   * &amp;lt;attribute name="textColThreshold"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
-   * name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&amp;gt;
-   * &amp;lt;attribute name="complementId"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
-   * name="showComplementFeatures"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
-   * &amp;lt;attribute name="showComplementFeaturesOnTop"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
-   * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(
-    name = "",
-    propOrder =
-    { "annotationColours", "hiddenColumns", "calcIdParam" })
-  public static class Viewport
-  {
-
-    @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
-    protected AnnotationColourScheme annotationColours;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
-
-    @XmlAttribute(name = "conservationSelected")
-    protected Boolean conservationSelected;
-
-    @XmlAttribute(name = "pidSelected")
-    protected Boolean pidSelected;
-
-    @XmlAttribute(name = "bgColour")
-    protected String bgColour;
-
-    @XmlAttribute(name = "consThreshold")
-    protected Integer consThreshold;
-
-    @XmlAttribute(name = "pidThreshold")
-    protected Integer pidThreshold;
-
-    @XmlAttribute(name = "title")
-    protected String title;
-
-    @XmlAttribute(name = "showFullId")
-    protected Boolean showFullId;
-
-    @XmlAttribute(name = "rightAlignIds")
-    protected Boolean rightAlignIds;
-
-    @XmlAttribute(name = "showText")
-    protected Boolean showText;
-
-    @XmlAttribute(name = "showColourText")
-    protected Boolean showColourText;
-
-    @XmlAttribute(name = "showUnconserved")
-    protected Boolean showUnconserved;
-
-    @XmlAttribute(name = "showBoxes")
-    protected Boolean showBoxes;
-
-    @XmlAttribute(name = "wrapAlignment")
-    protected Boolean wrapAlignment;
-
-    @XmlAttribute(name = "renderGaps")
-    protected Boolean renderGaps;
+        /**
+         * Gets the value of the threshold property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Float }
+         *     
+         */
+        public Float getThreshold() {
+            return threshold;
+        }
 
-    @XmlAttribute(name = "showSequenceFeatures")
-    protected Boolean showSequenceFeatures;
+        /**
+         * Sets the value of the threshold property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Float }
+         *     
+         */
+        public void setThreshold(Float value) {
+            this.threshold = value;
+        }
 
-    @XmlAttribute(name = "showNPfeatureTooltip")
-    protected Boolean showNPfeatureTooltip;
+        /**
+         * Gets the value of the showBootstrap property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowBootstrap() {
+            return showBootstrap;
+        }
 
-    @XmlAttribute(name = "showDbRefTooltip")
-    protected Boolean showDbRefTooltip;
+        /**
+         * Sets the value of the showBootstrap property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowBootstrap(Boolean value) {
+            this.showBootstrap = value;
+        }
 
-    @XmlAttribute(name = "followHighlight")
-    protected Boolean followHighlight;
+        /**
+         * Gets the value of the showDistances property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowDistances() {
+            return showDistances;
+        }
 
-    @XmlAttribute(name = "followSelection")
-    protected Boolean followSelection;
+        /**
+         * Sets the value of the showDistances property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowDistances(Boolean value) {
+            this.showDistances = value;
+        }
 
-    @XmlAttribute(name = "showAnnotation")
-    protected Boolean showAnnotation;
+        /**
+         * Gets the value of the markUnlinked property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isMarkUnlinked() {
+            return markUnlinked;
+        }
 
-    @XmlAttribute(name = "centreColumnLabels")
-    protected Boolean centreColumnLabels;
+        /**
+         * Sets the value of the markUnlinked property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setMarkUnlinked(Boolean value) {
+            this.markUnlinked = value;
+        }
 
-    @XmlAttribute(name = "showGroupConservation")
-    protected Boolean showGroupConservation;
+        /**
+         * Gets the value of the fitToWindow property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isFitToWindow() {
+            return fitToWindow;
+        }
 
-    @XmlAttribute(name = "showGroupConsensus")
-    protected Boolean showGroupConsensus;
+        /**
+         * Sets the value of the fitToWindow property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setFitToWindow(Boolean value) {
+            this.fitToWindow = value;
+        }
 
-    @XmlAttribute(name = "showConsensusHistogram")
-    protected Boolean showConsensusHistogram;
+        /**
+         * Gets the value of the currentTree property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isCurrentTree() {
+            return currentTree;
+        }
 
-    @XmlAttribute(name = "showSequenceLogo")
-    protected Boolean showSequenceLogo;
+        /**
+         * Sets the value of the currentTree property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setCurrentTree(Boolean value) {
+            this.currentTree = value;
+        }
 
-    @XmlAttribute(name = "normaliseSequenceLogo")
-    protected Boolean normaliseSequenceLogo;
+        /**
+         * Gets the value of the id property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getId() {
+            return id;
+        }
 
-    @XmlAttribute(name = "ignoreGapsinConsensus")
-    protected Boolean ignoreGapsinConsensus;
+        /**
+         * Sets the value of the id property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setId(String value) {
+            this.id = value;
+        }
 
-    @XmlAttribute(name = "startRes")
-    protected Integer startRes;
+        /**
+         * Gets the value of the linkToAllViews property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isLinkToAllViews() {
+            if (linkToAllViews == null) {
+                return false;
+            } else {
+                return linkToAllViews;
+            }
+        }
 
-    @XmlAttribute(name = "startSeq")
-    protected Integer startSeq;
+        /**
+         * Sets the value of the linkToAllViews property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setLinkToAllViews(Boolean value) {
+            this.linkToAllViews = value;
+        }
 
-    @XmlAttribute(name = "fontName")
-    protected String fontName;
+        /**
+         * Gets the value of the width property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getWidth() {
+            return width;
+        }
 
-    @XmlAttribute(name = "fontSize")
-    protected Integer fontSize;
+        /**
+         * Sets the value of the width property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setWidth(Integer value) {
+            this.width = value;
+        }
 
-    @XmlAttribute(name = "fontStyle")
-    protected Integer fontStyle;
+        /**
+         * Gets the value of the height property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getHeight() {
+            return height;
+        }
 
-    @XmlAttribute(name = "scaleProteinAsCdna")
-    protected Boolean scaleProteinAsCdna;
+        /**
+         * Sets the value of the height property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setHeight(Integer value) {
+            this.height = value;
+        }
 
-    @XmlAttribute(name = "viewName")
-    protected String viewName;
+        /**
+         * Gets the value of the xpos property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getXpos() {
+            return xpos;
+        }
 
-    @XmlAttribute(name = "sequenceSetId")
-    protected String sequenceSetId;
+        /**
+         * Sets the value of the xpos property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setXpos(Integer value) {
+            this.xpos = value;
+        }
 
-    @XmlAttribute(name = "gatheredViews")
-    protected Boolean gatheredViews;
+        /**
+         * Gets the value of the ypos property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getYpos() {
+            return ypos;
+        }
 
-    @XmlAttribute(name = "textCol1")
-    protected Integer textCol1;
+        /**
+         * Sets the value of the ypos property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setYpos(Integer value) {
+            this.ypos = value;
+        }
 
-    @XmlAttribute(name = "textCol2")
-    protected Integer textCol2;
+    }
 
-    @XmlAttribute(name = "textColThreshold")
-    protected Integer textColThreshold;
 
-    @XmlAttribute(name = "id")
-    @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
-    @XmlID
-    @XmlSchemaType(name = "ID")
-    protected String id;
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+     *       &lt;/sequence>
+     *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "userColourScheme"
+    })
+    public static class UserColours {
 
-    @XmlAttribute(name = "complementId")
-    protected String complementId;
+        @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
+        protected JalviewUserColours userColourScheme;
+        @XmlAttribute(name = "id")
+        protected String id;
 
-    @XmlAttribute(name = "showComplementFeatures")
-    protected Boolean showComplementFeatures;
+        /**
+         * Gets the value of the userColourScheme property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link JalviewUserColours }
+         *     
+         */
+        public JalviewUserColours getUserColourScheme() {
+            return userColourScheme;
+        }
 
-    @XmlAttribute(name = "showComplementFeaturesOnTop")
-    protected Boolean showComplementFeaturesOnTop;
+        /**
+         * Sets the value of the userColourScheme property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link JalviewUserColours }
+         *     
+         */
+        public void setUserColourScheme(JalviewUserColours value) {
+            this.userColourScheme = value;
+        }
 
-    @XmlAttribute(name = "width")
-    protected Integer width;
+        /**
+         * Gets the value of the id property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getId() {
+            return id;
+        }
 
-    @XmlAttribute(name = "height")
-    protected Integer height;
+        /**
+         * Sets the value of the id property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setId(String value) {
+            this.id = value;
+        }
 
-    @XmlAttribute(name = "xpos")
-    protected Integer xpos;
+    }
 
-    @XmlAttribute(name = "ypos")
-    protected Integer ypos;
 
     /**
-     * Gets the value of the annotationColours property.
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+     *         &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *               &lt;/restriction>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *         &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+     *                 &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *                 &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *               &lt;/extension>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *         &lt;element name="overview" minOccurs="0">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+     *                 &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *               &lt;/restriction>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *       &lt;/sequence>
+     *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+     *       &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+     *       &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
      * 
-     * @return possible object is {@link AnnotationColourScheme }
      * 
      */
-    public AnnotationColourScheme getAnnotationColours()
-    {
-      return annotationColours;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "annotationColours",
+        "hiddenColumns",
+        "calcIdParam",
+        "overview"
+    })
+    public static class Viewport {
+
+        @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
+        protected AnnotationColourScheme annotationColours;
+        @XmlElement(namespace = "www.jalview.org")
+        protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
+        @XmlElement(namespace = "www.jalview.org")
+        protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
+        @XmlElement(namespace = "www.jalview.org")
+        protected JalviewModel.Viewport.Overview overview;
+        @XmlAttribute(name = "conservationSelected")
+        protected Boolean conservationSelected;
+        @XmlAttribute(name = "pidSelected")
+        protected Boolean pidSelected;
+        @XmlAttribute(name = "bgColour")
+        protected String bgColour;
+        @XmlAttribute(name = "consThreshold")
+        protected Integer consThreshold;
+        @XmlAttribute(name = "pidThreshold")
+        protected Integer pidThreshold;
+        @XmlAttribute(name = "title")
+        protected String title;
+        @XmlAttribute(name = "showFullId")
+        protected Boolean showFullId;
+        @XmlAttribute(name = "rightAlignIds")
+        protected Boolean rightAlignIds;
+        @XmlAttribute(name = "showText")
+        protected Boolean showText;
+        @XmlAttribute(name = "showColourText")
+        protected Boolean showColourText;
+        @XmlAttribute(name = "showUnconserved")
+        protected Boolean showUnconserved;
+        @XmlAttribute(name = "showBoxes")
+        protected Boolean showBoxes;
+        @XmlAttribute(name = "wrapAlignment")
+        protected Boolean wrapAlignment;
+        @XmlAttribute(name = "renderGaps")
+        protected Boolean renderGaps;
+        @XmlAttribute(name = "showSequenceFeatures")
+        protected Boolean showSequenceFeatures;
+        @XmlAttribute(name = "showNPfeatureTooltip")
+        protected Boolean showNPfeatureTooltip;
+        @XmlAttribute(name = "showDbRefTooltip")
+        protected Boolean showDbRefTooltip;
+        @XmlAttribute(name = "followHighlight")
+        protected Boolean followHighlight;
+        @XmlAttribute(name = "followSelection")
+        protected Boolean followSelection;
+        @XmlAttribute(name = "showAnnotation")
+        protected Boolean showAnnotation;
+        @XmlAttribute(name = "centreColumnLabels")
+        protected Boolean centreColumnLabels;
+        @XmlAttribute(name = "showGroupConservation")
+        protected Boolean showGroupConservation;
+        @XmlAttribute(name = "showGroupConsensus")
+        protected Boolean showGroupConsensus;
+        @XmlAttribute(name = "showConsensusHistogram")
+        protected Boolean showConsensusHistogram;
+        @XmlAttribute(name = "showSequenceLogo")
+        protected Boolean showSequenceLogo;
+        @XmlAttribute(name = "normaliseSequenceLogo")
+        protected Boolean normaliseSequenceLogo;
+        @XmlAttribute(name = "ignoreGapsinConsensus")
+        protected Boolean ignoreGapsinConsensus;
+        @XmlAttribute(name = "startRes")
+        protected Integer startRes;
+        @XmlAttribute(name = "startSeq")
+        protected Integer startSeq;
+        @XmlAttribute(name = "fontName")
+        protected String fontName;
+        @XmlAttribute(name = "fontSize")
+        protected Integer fontSize;
+        @XmlAttribute(name = "fontStyle")
+        protected Integer fontStyle;
+        @XmlAttribute(name = "scaleProteinAsCdna")
+        protected Boolean scaleProteinAsCdna;
+        @XmlAttribute(name = "viewName")
+        protected String viewName;
+        @XmlAttribute(name = "sequenceSetId")
+        protected String sequenceSetId;
+        @XmlAttribute(name = "gatheredViews")
+        protected Boolean gatheredViews;
+        @XmlAttribute(name = "textCol1")
+        protected Integer textCol1;
+        @XmlAttribute(name = "textCol2")
+        protected Integer textCol2;
+        @XmlAttribute(name = "textColThreshold")
+        protected Integer textColThreshold;
+        @XmlAttribute(name = "id")
+        @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+        @XmlID
+        @XmlSchemaType(name = "ID")
+        protected String id;
+        @XmlAttribute(name = "complementId")
+        protected String complementId;
+        @XmlAttribute(name = "showComplementFeatures")
+        protected Boolean showComplementFeatures;
+        @XmlAttribute(name = "showComplementFeaturesOnTop")
+        protected Boolean showComplementFeaturesOnTop;
+        @XmlAttribute(name = "width")
+        protected Integer width;
+        @XmlAttribute(name = "height")
+        protected Integer height;
+        @XmlAttribute(name = "xpos")
+        protected Integer xpos;
+        @XmlAttribute(name = "ypos")
+        protected Integer ypos;
 
-    /**
-     * Sets the value of the annotationColours property.
-     * 
-     * @param value
-     *          allowed object is {@link AnnotationColourScheme }
-     * 
-     */
-    public void setAnnotationColours(AnnotationColourScheme value)
-    {
-      this.annotationColours = value;
-    }
+        /**
+         * Gets the value of the annotationColours property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link AnnotationColourScheme }
+         *     
+         */
+        public AnnotationColourScheme getAnnotationColours() {
+            return annotationColours;
+        }
 
-    /**
-     * Gets the value of the hiddenColumns property.
-     * 
-     * &lt;p&gt; This accessor method returns a reference to the live list, not
-     * a snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * &lt;CODE&gt;set&lt;/CODE&gt; method for the hiddenColumns property.
-     * 
-     * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-     * getHiddenColumns().add(newItem); &lt;/pre&gt;
-     * 
-     * 
-     * &lt;p&gt; Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.Viewport.HiddenColumns }
-     * 
-     * 
-     */
-    public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns()
-    {
-      if (hiddenColumns == null)
-      {
-        hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
-      }
-      return this.hiddenColumns;
-    }
+        /**
+         * Sets the value of the annotationColours property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link AnnotationColourScheme }
+         *     
+         */
+        public void setAnnotationColours(AnnotationColourScheme value) {
+            this.annotationColours = value;
+        }
 
-    /**
-     * Gets the value of the calcIdParam property.
-     * 
-     * &lt;p&gt; This accessor method returns a reference to the live list, not
-     * a snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * &lt;CODE&gt;set&lt;/CODE&gt; method for the calcIdParam property.
-     * 
-     * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-     * getCalcIdParam().add(newItem); &lt;/pre&gt;
-     * 
-     * 
-     * &lt;p&gt; Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.Viewport.CalcIdParam }
-     * 
-     * 
-     */
-    public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam()
-    {
-      if (calcIdParam == null)
-      {
-        calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
-      }
-      return this.calcIdParam;
-    }
+        /**
+         * Gets the value of the hiddenColumns property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getHiddenColumns().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.Viewport.HiddenColumns }
+         * 
+         * 
+         */
+        public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
+            if (hiddenColumns == null) {
+                hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
+            }
+            return this.hiddenColumns;
+        }
 
-    /**
-     * Gets the value of the conservationSelected property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isConservationSelected()
-    {
-      return conservationSelected;
-    }
+        /**
+         * Gets the value of the calcIdParam property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getCalcIdParam().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.Viewport.CalcIdParam }
+         * 
+         * 
+         */
+        public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
+            if (calcIdParam == null) {
+                calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
+            }
+            return this.calcIdParam;
+        }
 
-    /**
-     * Sets the value of the conservationSelected property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setConservationSelected(Boolean value)
-    {
-      this.conservationSelected = value;
-    }
+        /**
+         * Gets the value of the overview property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link JalviewModel.Viewport.Overview }
+         *     
+         */
+        public JalviewModel.Viewport.Overview getOverview() {
+            return overview;
+        }
 
-    /**
-     * Gets the value of the pidSelected property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isPidSelected()
-    {
-      return pidSelected;
-    }
+        /**
+         * Sets the value of the overview property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link JalviewModel.Viewport.Overview }
+         *     
+         */
+        public void setOverview(JalviewModel.Viewport.Overview value) {
+            this.overview = value;
+        }
 
-    /**
-     * Sets the value of the pidSelected property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setPidSelected(Boolean value)
-    {
-      this.pidSelected = value;
-    }
+        /**
+         * Gets the value of the conservationSelected property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isConservationSelected() {
+            return conservationSelected;
+        }
 
-    /**
-     * Gets the value of the bgColour property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getBgColour()
-    {
-      return bgColour;
-    }
+        /**
+         * Sets the value of the conservationSelected property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setConservationSelected(Boolean value) {
+            this.conservationSelected = value;
+        }
 
-    /**
-     * Sets the value of the bgColour property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setBgColour(String value)
-    {
-      this.bgColour = value;
-    }
+        /**
+         * Gets the value of the pidSelected property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isPidSelected() {
+            return pidSelected;
+        }
 
-    /**
-     * Gets the value of the consThreshold property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getConsThreshold()
-    {
-      return consThreshold;
-    }
+        /**
+         * Sets the value of the pidSelected property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setPidSelected(Boolean value) {
+            this.pidSelected = value;
+        }
 
-    /**
-     * Sets the value of the consThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setConsThreshold(Integer value)
-    {
-      this.consThreshold = value;
-    }
+        /**
+         * Gets the value of the bgColour property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getBgColour() {
+            return bgColour;
+        }
 
-    /**
-     * Gets the value of the pidThreshold property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getPidThreshold()
-    {
-      return pidThreshold;
-    }
+        /**
+         * Sets the value of the bgColour property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setBgColour(String value) {
+            this.bgColour = value;
+        }
 
-    /**
-     * Sets the value of the pidThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setPidThreshold(Integer value)
-    {
-      this.pidThreshold = value;
-    }
+        /**
+         * Gets the value of the consThreshold property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getConsThreshold() {
+            return consThreshold;
+        }
 
-    /**
-     * Gets the value of the title property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getTitle()
-    {
-      return title;
-    }
+        /**
+         * Sets the value of the consThreshold property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setConsThreshold(Integer value) {
+            this.consThreshold = value;
+        }
 
-    /**
-     * Sets the value of the title property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setTitle(String value)
-    {
-      this.title = value;
-    }
+        /**
+         * Gets the value of the pidThreshold property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getPidThreshold() {
+            return pidThreshold;
+        }
 
-    /**
-     * Gets the value of the showFullId property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowFullId()
-    {
-      return showFullId;
-    }
+        /**
+         * Sets the value of the pidThreshold property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setPidThreshold(Integer value) {
+            this.pidThreshold = value;
+        }
 
-    /**
-     * Sets the value of the showFullId property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowFullId(Boolean value)
-    {
-      this.showFullId = value;
-    }
+        /**
+         * Gets the value of the title property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getTitle() {
+            return title;
+        }
 
-    /**
-     * Gets the value of the rightAlignIds property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isRightAlignIds()
-    {
-      return rightAlignIds;
-    }
+        /**
+         * Sets the value of the title property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setTitle(String value) {
+            this.title = value;
+        }
 
-    /**
-     * Sets the value of the rightAlignIds property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setRightAlignIds(Boolean value)
-    {
-      this.rightAlignIds = value;
-    }
+        /**
+         * Gets the value of the showFullId property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowFullId() {
+            return showFullId;
+        }
 
-    /**
-     * Gets the value of the showText property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowText()
-    {
-      return showText;
-    }
+        /**
+         * Sets the value of the showFullId property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowFullId(Boolean value) {
+            this.showFullId = value;
+        }
 
-    /**
-     * Sets the value of the showText property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowText(Boolean value)
-    {
-      this.showText = value;
-    }
+        /**
+         * Gets the value of the rightAlignIds property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isRightAlignIds() {
+            return rightAlignIds;
+        }
 
-    /**
-     * Gets the value of the showColourText property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowColourText()
-    {
-      return showColourText;
-    }
+        /**
+         * Sets the value of the rightAlignIds property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setRightAlignIds(Boolean value) {
+            this.rightAlignIds = value;
+        }
 
-    /**
-     * Sets the value of the showColourText property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowColourText(Boolean value)
-    {
-      this.showColourText = value;
-    }
+        /**
+         * Gets the value of the showText property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowText() {
+            return showText;
+        }
+
+        /**
+         * Sets the value of the showText property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowText(Boolean value) {
+            this.showText = value;
+        }
+
+        /**
+         * Gets the value of the showColourText property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowColourText() {
+            return showColourText;
+        }
+
+        /**
+         * Sets the value of the showColourText property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowColourText(Boolean value) {
+            this.showColourText = value;
+        }
+
+        /**
+         * Gets the value of the showUnconserved property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowUnconserved() {
+            if (showUnconserved == null) {
+                return false;
+            } else {
+                return showUnconserved;
+            }
+        }
+
+        /**
+         * Sets the value of the showUnconserved property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowUnconserved(Boolean value) {
+            this.showUnconserved = value;
+        }
+
+        /**
+         * Gets the value of the showBoxes property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowBoxes() {
+            return showBoxes;
+        }
+
+        /**
+         * Sets the value of the showBoxes property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowBoxes(Boolean value) {
+            this.showBoxes = value;
+        }
+
+        /**
+         * Gets the value of the wrapAlignment property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isWrapAlignment() {
+            return wrapAlignment;
+        }
 
-    /**
-     * Gets the value of the showUnconserved property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowUnconserved()
-    {
-      if (showUnconserved == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showUnconserved;
-      }
-    }
+        /**
+         * Sets the value of the wrapAlignment property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setWrapAlignment(Boolean value) {
+            this.wrapAlignment = value;
+        }
 
-    /**
-     * Sets the value of the showUnconserved property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowUnconserved(Boolean value)
-    {
-      this.showUnconserved = value;
-    }
+        /**
+         * Gets the value of the renderGaps property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isRenderGaps() {
+            return renderGaps;
+        }
 
-    /**
-     * Gets the value of the showBoxes property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowBoxes()
-    {
-      return showBoxes;
-    }
+        /**
+         * Sets the value of the renderGaps property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setRenderGaps(Boolean value) {
+            this.renderGaps = value;
+        }
 
-    /**
-     * Sets the value of the showBoxes property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowBoxes(Boolean value)
-    {
-      this.showBoxes = value;
-    }
+        /**
+         * Gets the value of the showSequenceFeatures property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowSequenceFeatures() {
+            return showSequenceFeatures;
+        }
 
-    /**
-     * Gets the value of the wrapAlignment property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isWrapAlignment()
-    {
-      return wrapAlignment;
-    }
+        /**
+         * Sets the value of the showSequenceFeatures property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowSequenceFeatures(Boolean value) {
+            this.showSequenceFeatures = value;
+        }
 
-    /**
-     * Sets the value of the wrapAlignment property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setWrapAlignment(Boolean value)
-    {
-      this.wrapAlignment = value;
-    }
+        /**
+         * Gets the value of the showNPfeatureTooltip property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowNPfeatureTooltip() {
+            return showNPfeatureTooltip;
+        }
 
-    /**
-     * Gets the value of the renderGaps property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isRenderGaps()
-    {
-      return renderGaps;
-    }
+        /**
+         * Sets the value of the showNPfeatureTooltip property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowNPfeatureTooltip(Boolean value) {
+            this.showNPfeatureTooltip = value;
+        }
 
-    /**
-     * Sets the value of the renderGaps property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setRenderGaps(Boolean value)
-    {
-      this.renderGaps = value;
-    }
+        /**
+         * Gets the value of the showDbRefTooltip property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowDbRefTooltip() {
+            return showDbRefTooltip;
+        }
 
-    /**
-     * Gets the value of the showSequenceFeatures property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowSequenceFeatures()
-    {
-      return showSequenceFeatures;
-    }
+        /**
+         * Sets the value of the showDbRefTooltip property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowDbRefTooltip(Boolean value) {
+            this.showDbRefTooltip = value;
+        }
 
-    /**
-     * Sets the value of the showSequenceFeatures property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowSequenceFeatures(Boolean value)
-    {
-      this.showSequenceFeatures = value;
-    }
+        /**
+         * Gets the value of the followHighlight property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isFollowHighlight() {
+            if (followHighlight == null) {
+                return true;
+            } else {
+                return followHighlight;
+            }
+        }
 
-    /**
-     * Gets the value of the showNPfeatureTooltip property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowNPfeatureTooltip()
-    {
-      return showNPfeatureTooltip;
-    }
+        /**
+         * Sets the value of the followHighlight property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setFollowHighlight(Boolean value) {
+            this.followHighlight = value;
+        }
 
-    /**
-     * Sets the value of the showNPfeatureTooltip property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowNPfeatureTooltip(Boolean value)
-    {
-      this.showNPfeatureTooltip = value;
-    }
+        /**
+         * Gets the value of the followSelection property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isFollowSelection() {
+            if (followSelection == null) {
+                return true;
+            } else {
+                return followSelection;
+            }
+        }
 
-    /**
-     * Gets the value of the showDbRefTooltip property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowDbRefTooltip()
-    {
-      return showDbRefTooltip;
-    }
+        /**
+         * Sets the value of the followSelection property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setFollowSelection(Boolean value) {
+            this.followSelection = value;
+        }
 
-    /**
-     * Sets the value of the showDbRefTooltip property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowDbRefTooltip(Boolean value)
-    {
-      this.showDbRefTooltip = value;
-    }
+        /**
+         * Gets the value of the showAnnotation property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowAnnotation() {
+            return showAnnotation;
+        }
 
-    /**
-     * Gets the value of the followHighlight property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isFollowHighlight()
-    {
-      if (followHighlight == null)
-      {
-        return true;
-      }
-      else
-      {
-        return followHighlight;
-      }
-    }
+        /**
+         * Sets the value of the showAnnotation property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowAnnotation(Boolean value) {
+            this.showAnnotation = value;
+        }
 
-    /**
-     * Sets the value of the followHighlight property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setFollowHighlight(Boolean value)
-    {
-      this.followHighlight = value;
-    }
+        /**
+         * Gets the value of the centreColumnLabels property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isCentreColumnLabels() {
+            if (centreColumnLabels == null) {
+                return false;
+            } else {
+                return centreColumnLabels;
+            }
+        }
 
-    /**
-     * Gets the value of the followSelection property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isFollowSelection()
-    {
-      if (followSelection == null)
-      {
-        return true;
-      }
-      else
-      {
-        return followSelection;
-      }
-    }
+        /**
+         * Sets the value of the centreColumnLabels property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setCentreColumnLabels(Boolean value) {
+            this.centreColumnLabels = value;
+        }
 
-    /**
-     * Sets the value of the followSelection property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setFollowSelection(Boolean value)
-    {
-      this.followSelection = value;
-    }
+        /**
+         * Gets the value of the showGroupConservation property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowGroupConservation() {
+            if (showGroupConservation == null) {
+                return false;
+            } else {
+                return showGroupConservation;
+            }
+        }
 
-    /**
-     * Gets the value of the showAnnotation property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowAnnotation()
-    {
-      return showAnnotation;
-    }
+        /**
+         * Sets the value of the showGroupConservation property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowGroupConservation(Boolean value) {
+            this.showGroupConservation = value;
+        }
 
-    /**
-     * Sets the value of the showAnnotation property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowAnnotation(Boolean value)
-    {
-      this.showAnnotation = value;
-    }
+        /**
+         * Gets the value of the showGroupConsensus property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowGroupConsensus() {
+            if (showGroupConsensus == null) {
+                return false;
+            } else {
+                return showGroupConsensus;
+            }
+        }
 
-    /**
-     * Gets the value of the centreColumnLabels property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isCentreColumnLabels()
-    {
-      if (centreColumnLabels == null)
-      {
-        return false;
-      }
-      else
-      {
-        return centreColumnLabels;
-      }
-    }
+        /**
+         * Sets the value of the showGroupConsensus property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowGroupConsensus(Boolean value) {
+            this.showGroupConsensus = value;
+        }
 
-    /**
-     * Sets the value of the centreColumnLabels property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setCentreColumnLabels(Boolean value)
-    {
-      this.centreColumnLabels = value;
-    }
+        /**
+         * Gets the value of the showConsensusHistogram property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowConsensusHistogram() {
+            if (showConsensusHistogram == null) {
+                return true;
+            } else {
+                return showConsensusHistogram;
+            }
+        }
 
-    /**
-     * Gets the value of the showGroupConservation property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowGroupConservation()
-    {
-      if (showGroupConservation == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showGroupConservation;
-      }
-    }
+        /**
+         * Sets the value of the showConsensusHistogram property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowConsensusHistogram(Boolean value) {
+            this.showConsensusHistogram = value;
+        }
 
-    /**
-     * Sets the value of the showGroupConservation property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowGroupConservation(Boolean value)
-    {
-      this.showGroupConservation = value;
-    }
+        /**
+         * Gets the value of the showSequenceLogo property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowSequenceLogo() {
+            if (showSequenceLogo == null) {
+                return false;
+            } else {
+                return showSequenceLogo;
+            }
+        }
 
-    /**
-     * Gets the value of the showGroupConsensus property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowGroupConsensus()
-    {
-      if (showGroupConsensus == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showGroupConsensus;
-      }
-    }
+        /**
+         * Sets the value of the showSequenceLogo property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowSequenceLogo(Boolean value) {
+            this.showSequenceLogo = value;
+        }
+
+        /**
+         * Gets the value of the normaliseSequenceLogo property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isNormaliseSequenceLogo() {
+            if (normaliseSequenceLogo == null) {
+                return false;
+            } else {
+                return normaliseSequenceLogo;
+            }
+        }
 
-    /**
-     * Sets the value of the showGroupConsensus property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowGroupConsensus(Boolean value)
-    {
-      this.showGroupConsensus = value;
-    }
+        /**
+         * Sets the value of the normaliseSequenceLogo property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setNormaliseSequenceLogo(Boolean value) {
+            this.normaliseSequenceLogo = value;
+        }
 
-    /**
-     * Gets the value of the showConsensusHistogram property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowConsensusHistogram()
-    {
-      if (showConsensusHistogram == null)
-      {
-        return true;
-      }
-      else
-      {
-        return showConsensusHistogram;
-      }
-    }
+        /**
+         * Gets the value of the ignoreGapsinConsensus property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isIgnoreGapsinConsensus() {
+            if (ignoreGapsinConsensus == null) {
+                return true;
+            } else {
+                return ignoreGapsinConsensus;
+            }
+        }
 
-    /**
-     * Sets the value of the showConsensusHistogram property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowConsensusHistogram(Boolean value)
-    {
-      this.showConsensusHistogram = value;
-    }
+        /**
+         * Sets the value of the ignoreGapsinConsensus property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setIgnoreGapsinConsensus(Boolean value) {
+            this.ignoreGapsinConsensus = value;
+        }
 
-    /**
-     * Gets the value of the showSequenceLogo property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowSequenceLogo()
-    {
-      if (showSequenceLogo == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showSequenceLogo;
-      }
-    }
+        /**
+         * Gets the value of the startRes property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getStartRes() {
+            return startRes;
+        }
 
-    /**
-     * Sets the value of the showSequenceLogo property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowSequenceLogo(Boolean value)
-    {
-      this.showSequenceLogo = value;
-    }
+        /**
+         * Sets the value of the startRes property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setStartRes(Integer value) {
+            this.startRes = value;
+        }
 
-    /**
-     * Gets the value of the normaliseSequenceLogo property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isNormaliseSequenceLogo()
-    {
-      if (normaliseSequenceLogo == null)
-      {
-        return false;
-      }
-      else
-      {
-        return normaliseSequenceLogo;
-      }
-    }
+        /**
+         * Gets the value of the startSeq property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getStartSeq() {
+            return startSeq;
+        }
 
-    /**
-     * Sets the value of the normaliseSequenceLogo property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setNormaliseSequenceLogo(Boolean value)
-    {
-      this.normaliseSequenceLogo = value;
-    }
+        /**
+         * Sets the value of the startSeq property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setStartSeq(Integer value) {
+            this.startSeq = value;
+        }
 
-    /**
-     * Gets the value of the ignoreGapsinConsensus property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isIgnoreGapsinConsensus()
-    {
-      if (ignoreGapsinConsensus == null)
-      {
-        return true;
-      }
-      else
-      {
-        return ignoreGapsinConsensus;
-      }
-    }
+        /**
+         * Gets the value of the fontName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getFontName() {
+            return fontName;
+        }
 
-    /**
-     * Sets the value of the ignoreGapsinConsensus property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setIgnoreGapsinConsensus(Boolean value)
-    {
-      this.ignoreGapsinConsensus = value;
-    }
+        /**
+         * Sets the value of the fontName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setFontName(String value) {
+            this.fontName = value;
+        }
 
-    /**
-     * Gets the value of the startRes property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getStartRes()
-    {
-      return startRes;
-    }
+        /**
+         * Gets the value of the fontSize property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getFontSize() {
+            return fontSize;
+        }
 
-    /**
-     * Sets the value of the startRes property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setStartRes(Integer value)
-    {
-      this.startRes = value;
-    }
+        /**
+         * Sets the value of the fontSize property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setFontSize(Integer value) {
+            this.fontSize = value;
+        }
 
-    /**
-     * Gets the value of the startSeq property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getStartSeq()
-    {
-      return startSeq;
-    }
+        /**
+         * Gets the value of the fontStyle property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getFontStyle() {
+            return fontStyle;
+        }
 
-    /**
-     * Sets the value of the startSeq property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setStartSeq(Integer value)
-    {
-      this.startSeq = value;
-    }
+        /**
+         * Sets the value of the fontStyle property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setFontStyle(Integer value) {
+            this.fontStyle = value;
+        }
 
-    /**
-     * Gets the value of the fontName property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getFontName()
-    {
-      return fontName;
-    }
+        /**
+         * Gets the value of the scaleProteinAsCdna property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isScaleProteinAsCdna() {
+            if (scaleProteinAsCdna == null) {
+                return true;
+            } else {
+                return scaleProteinAsCdna;
+            }
+        }
 
-    /**
-     * Sets the value of the fontName property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setFontName(String value)
-    {
-      this.fontName = value;
-    }
+        /**
+         * Sets the value of the scaleProteinAsCdna property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setScaleProteinAsCdna(Boolean value) {
+            this.scaleProteinAsCdna = value;
+        }
 
-    /**
-     * Gets the value of the fontSize property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getFontSize()
-    {
-      return fontSize;
-    }
+        /**
+         * Gets the value of the viewName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getViewName() {
+            return viewName;
+        }
 
-    /**
-     * Sets the value of the fontSize property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setFontSize(Integer value)
-    {
-      this.fontSize = value;
-    }
+        /**
+         * Sets the value of the viewName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setViewName(String value) {
+            this.viewName = value;
+        }
 
-    /**
-     * Gets the value of the fontStyle property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getFontStyle()
-    {
-      return fontStyle;
-    }
+        /**
+         * Gets the value of the sequenceSetId property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getSequenceSetId() {
+            return sequenceSetId;
+        }
 
-    /**
-     * Sets the value of the fontStyle property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setFontStyle(Integer value)
-    {
-      this.fontStyle = value;
-    }
+        /**
+         * Sets the value of the sequenceSetId property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setSequenceSetId(String value) {
+            this.sequenceSetId = value;
+        }
 
-    /**
-     * Gets the value of the scaleProteinAsCdna property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isScaleProteinAsCdna()
-    {
-      if (scaleProteinAsCdna == null)
-      {
-        return true;
-      }
-      else
-      {
-        return scaleProteinAsCdna;
-      }
-    }
+        /**
+         * Gets the value of the gatheredViews property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isGatheredViews() {
+            return gatheredViews;
+        }
 
-    /**
-     * Sets the value of the scaleProteinAsCdna property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setScaleProteinAsCdna(Boolean value)
-    {
-      this.scaleProteinAsCdna = value;
-    }
+        /**
+         * Sets the value of the gatheredViews property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setGatheredViews(Boolean value) {
+            this.gatheredViews = value;
+        }
 
-    /**
-     * Gets the value of the viewName property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getViewName()
-    {
-      return viewName;
-    }
+        /**
+         * Gets the value of the textCol1 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getTextCol1() {
+            return textCol1;
+        }
 
-    /**
-     * Sets the value of the viewName property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setViewName(String value)
-    {
-      this.viewName = value;
-    }
+        /**
+         * Sets the value of the textCol1 property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setTextCol1(Integer value) {
+            this.textCol1 = value;
+        }
 
-    /**
-     * Gets the value of the sequenceSetId property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getSequenceSetId()
-    {
-      return sequenceSetId;
-    }
+        /**
+         * Gets the value of the textCol2 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getTextCol2() {
+            return textCol2;
+        }
 
-    /**
-     * Sets the value of the sequenceSetId property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setSequenceSetId(String value)
-    {
-      this.sequenceSetId = value;
-    }
+        /**
+         * Sets the value of the textCol2 property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setTextCol2(Integer value) {
+            this.textCol2 = value;
+        }
 
-    /**
-     * Gets the value of the gatheredViews property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isGatheredViews()
-    {
-      return gatheredViews;
-    }
+        /**
+         * Gets the value of the textColThreshold property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getTextColThreshold() {
+            return textColThreshold;
+        }
 
-    /**
-     * Sets the value of the gatheredViews property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setGatheredViews(Boolean value)
-    {
-      this.gatheredViews = value;
-    }
+        /**
+         * Sets the value of the textColThreshold property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setTextColThreshold(Integer value) {
+            this.textColThreshold = value;
+        }
 
-    /**
-     * Gets the value of the textCol1 property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getTextCol1()
-    {
-      return textCol1;
-    }
+        /**
+         * Gets the value of the id property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getId() {
+            return id;
+        }
 
-    /**
-     * Sets the value of the textCol1 property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextCol1(Integer value)
-    {
-      this.textCol1 = value;
-    }
+        /**
+         * Sets the value of the id property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setId(String value) {
+            this.id = value;
+        }
 
-    /**
-     * Gets the value of the textCol2 property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getTextCol2()
-    {
-      return textCol2;
-    }
+        /**
+         * Gets the value of the complementId property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getComplementId() {
+            return complementId;
+        }
 
-    /**
-     * Sets the value of the textCol2 property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextCol2(Integer value)
-    {
-      this.textCol2 = value;
-    }
+        /**
+         * Sets the value of the complementId property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setComplementId(String value) {
+            this.complementId = value;
+        }
 
-    /**
-     * Gets the value of the textColThreshold property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getTextColThreshold()
-    {
-      return textColThreshold;
-    }
+        /**
+         * Gets the value of the showComplementFeatures property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowComplementFeatures() {
+            if (showComplementFeatures == null) {
+                return false;
+            } else {
+                return showComplementFeatures;
+            }
+        }
 
-    /**
-     * Sets the value of the textColThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextColThreshold(Integer value)
-    {
-      this.textColThreshold = value;
-    }
+        /**
+         * Sets the value of the showComplementFeatures property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowComplementFeatures(Boolean value) {
+            this.showComplementFeatures = value;
+        }
 
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getId()
-    {
-      return id;
-    }
+        /**
+         * Gets the value of the showComplementFeaturesOnTop property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowComplementFeaturesOnTop() {
+            if (showComplementFeaturesOnTop == null) {
+                return false;
+            } else {
+                return showComplementFeaturesOnTop;
+            }
+        }
 
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setId(String value)
-    {
-      this.id = value;
-    }
+        /**
+         * Sets the value of the showComplementFeaturesOnTop property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowComplementFeaturesOnTop(Boolean value) {
+            this.showComplementFeaturesOnTop = value;
+        }
 
-    /**
-     * Gets the value of the complementId property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getComplementId()
-    {
-      return complementId;
-    }
+        /**
+         * Gets the value of the width property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getWidth() {
+            return width;
+        }
 
-    /**
-     * Sets the value of the complementId property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setComplementId(String value)
-    {
-      this.complementId = value;
-    }
+        /**
+         * Sets the value of the width property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setWidth(Integer value) {
+            this.width = value;
+        }
 
-    /**
-     * Gets the value of the showComplementFeatures property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowComplementFeatures()
-    {
-      if (showComplementFeatures == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showComplementFeatures;
-      }
-    }
+        /**
+         * Gets the value of the height property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getHeight() {
+            return height;
+        }
 
-    /**
-     * Sets the value of the showComplementFeatures property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowComplementFeatures(Boolean value)
-    {
-      this.showComplementFeatures = value;
-    }
+        /**
+         * Sets the value of the height property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setHeight(Integer value) {
+            this.height = value;
+        }
 
-    /**
-     * Gets the value of the showComplementFeaturesOnTop property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowComplementFeaturesOnTop()
-    {
-      if (showComplementFeaturesOnTop == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showComplementFeaturesOnTop;
-      }
-    }
+        /**
+         * Gets the value of the xpos property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getXpos() {
+            return xpos;
+        }
 
-    /**
-     * Sets the value of the showComplementFeaturesOnTop property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowComplementFeaturesOnTop(Boolean value)
-    {
-      this.showComplementFeaturesOnTop = value;
-    }
+        /**
+         * Sets the value of the xpos property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setXpos(Integer value) {
+            this.xpos = value;
+        }
 
-    /**
-     * Gets the value of the width property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getWidth()
-    {
-      return width;
-    }
+        /**
+         * Gets the value of the ypos property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getYpos() {
+            return ypos;
+        }
 
-    /**
-     * Sets the value of the width property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setWidth(Integer value)
-    {
-      this.width = value;
-    }
+        /**
+         * Sets the value of the ypos property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setYpos(Integer value) {
+            this.ypos = value;
+        }
 
-    /**
-     * Gets the value of the height property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getHeight()
-    {
-      return height;
-    }
 
-    /**
-     * Sets the value of the height property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setHeight(Integer value)
-    {
-      this.height = value;
-    }
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+         *       &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+         *       &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *     &lt;/extension>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class CalcIdParam
+            extends WebServiceParameterSet
+        {
 
-    /**
-     * Gets the value of the xpos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getXpos()
-    {
-      return xpos;
-    }
+            @XmlAttribute(name = "calcId", required = true)
+            protected String calcId;
+            @XmlAttribute(name = "needsUpdate")
+            protected Boolean needsUpdate;
+            @XmlAttribute(name = "autoUpdate", required = true)
+            protected boolean autoUpdate;
+
+            /**
+             * Gets the value of the calcId property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getCalcId() {
+                return calcId;
+            }
+
+            /**
+             * Sets the value of the calcId property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setCalcId(String value) {
+                this.calcId = value;
+            }
+
+            /**
+             * Gets the value of the needsUpdate property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Boolean }
+             *     
+             */
+            public boolean isNeedsUpdate() {
+                if (needsUpdate == null) {
+                    return false;
+                } else {
+                    return needsUpdate;
+                }
+            }
+
+            /**
+             * Sets the value of the needsUpdate property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Boolean }
+             *     
+             */
+            public void setNeedsUpdate(Boolean value) {
+                this.needsUpdate = value;
+            }
+
+            /**
+             * Gets the value of the autoUpdate property.
+             * 
+             */
+            public boolean isAutoUpdate() {
+                return autoUpdate;
+            }
+
+            /**
+             * Sets the value of the autoUpdate property.
+             * 
+             */
+            public void setAutoUpdate(boolean value) {
+                this.autoUpdate = value;
+            }
 
-    /**
-     * Sets the value of the xpos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setXpos(Integer value)
-    {
-      this.xpos = value;
-    }
+        }
 
-    /**
-     * Gets the value of the ypos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getYpos()
-    {
-      return ypos;
-    }
 
-    /**
-     * Sets the value of the ypos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setYpos(Integer value)
-    {
-      this.ypos = value;
-    }
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *     &lt;/restriction>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class HiddenColumns {
+
+            @XmlAttribute(name = "start")
+            protected Integer start;
+            @XmlAttribute(name = "end")
+            protected Integer end;
+
+            /**
+             * Gets the value of the start property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getStart() {
+                return start;
+            }
+
+            /**
+             * Sets the value of the start property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setStart(Integer value) {
+                this.start = value;
+            }
+
+            /**
+             * Gets the value of the end property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getEnd() {
+                return end;
+            }
+
+            /**
+             * Sets the value of the end property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setEnd(Integer value) {
+                this.end = value;
+            }
 
-    /**
-     * &lt;p&gt;Java class for anonymous complex type.
-     * 
-     * &lt;p&gt;The following schema fragment specifies the expected content
-     * contained within this class.
-     * 
-     * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-     * &amp;lt;extension
-     * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&amp;gt;
-     * &amp;lt;attribute name="calcId" use="required"
-     * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-     * &amp;lt;attribute name="needsUpdate"
-     * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
-     * /&amp;gt; &amp;lt;attribute name="autoUpdate" use="required"
-     * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-     * &amp;lt;/extension&amp;gt; &amp;lt;/complexContent&amp;gt;
-     * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class CalcIdParam extends WebServiceParameterSet
-    {
-
-      @XmlAttribute(name = "calcId", required = true)
-      protected String calcId;
-
-      @XmlAttribute(name = "needsUpdate")
-      protected Boolean needsUpdate;
-
-      @XmlAttribute(name = "autoUpdate", required = true)
-      protected boolean autoUpdate;
-
-      /**
-       * Gets the value of the calcId property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getCalcId()
-      {
-        return calcId;
-      }
-
-      /**
-       * Sets the value of the calcId property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setCalcId(String value)
-      {
-        this.calcId = value;
-      }
-
-      /**
-       * Gets the value of the needsUpdate property.
-       * 
-       * @return possible object is {@link Boolean }
-       * 
-       */
-      public boolean isNeedsUpdate()
-      {
-        if (needsUpdate == null)
-        {
-          return false;
         }
-        else
-        {
-          return needsUpdate;
-        }
-      }
-
-      /**
-       * Sets the value of the needsUpdate property.
-       * 
-       * @param value
-       *          allowed object is {@link Boolean }
-       * 
-       */
-      public void setNeedsUpdate(Boolean value)
-      {
-        this.needsUpdate = value;
-      }
-
-      /**
-       * Gets the value of the autoUpdate property.
-       * 
-       */
-      public boolean isAutoUpdate()
-      {
-        return autoUpdate;
-      }
-
-      /**
-       * Sets the value of the autoUpdate property.
-       * 
-       */
-      public void setAutoUpdate(boolean value)
-      {
-        this.autoUpdate = value;
-      }
 
-    }
 
-    /**
-     * &lt;p&gt;Java class for anonymous complex type.
-     * 
-     * &lt;p&gt;The following schema fragment specifies the expected content
-     * contained within this class.
-     * 
-     * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-     * &amp;lt;restriction
-     * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
-     * &amp;lt;attribute name="start"
-     * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
-     * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
-     * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-     * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class HiddenColumns
-    {
-
-      @XmlAttribute(name = "start")
-      protected Integer start;
-
-      @XmlAttribute(name = "end")
-      protected Integer end;
-
-      /**
-       * Gets the value of the start property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getStart()
-      {
-        return start;
-      }
-
-      /**
-       * Sets the value of the start property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setStart(Integer value)
-      {
-        this.start = value;
-      }
-
-      /**
-       * Gets the value of the end property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getEnd()
-      {
-        return end;
-      }
-
-      /**
-       * Sets the value of the end property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setEnd(Integer value)
-      {
-        this.end = value;
-      }
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+         *       &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *       &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *     &lt;/restriction>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class Overview {
+
+            @XmlAttribute(name = "showHidden")
+            protected Boolean showHidden;
+            @XmlAttribute(name = "residueColour")
+            protected Integer residueColour;
+            @XmlAttribute(name = "gapColour")
+            protected Integer gapColour;
+            @XmlAttribute(name = "hiddenColour")
+            protected Integer hiddenColour;
+            @XmlAttribute(name = "title")
+            protected String title;
+            @XmlAttribute(name = "width")
+            protected Integer width;
+            @XmlAttribute(name = "height")
+            protected Integer height;
+            @XmlAttribute(name = "xpos")
+            protected Integer xpos;
+            @XmlAttribute(name = "ypos")
+            protected Integer ypos;
+
+            /**
+             * Gets the value of the showHidden property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Boolean }
+             *     
+             */
+            public Boolean isShowHidden() {
+                return showHidden;
+            }
+
+            /**
+             * Sets the value of the showHidden property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Boolean }
+             *     
+             */
+            public void setShowHidden(Boolean value) {
+                this.showHidden = value;
+            }
+
+            /**
+             * Gets the value of the residueColour property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getResidueColour() {
+                return residueColour;
+            }
+
+            /**
+             * Sets the value of the residueColour property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setResidueColour(Integer value) {
+                this.residueColour = value;
+            }
+
+            /**
+             * Gets the value of the gapColour property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getGapColour() {
+                return gapColour;
+            }
+
+            /**
+             * Sets the value of the gapColour property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setGapColour(Integer value) {
+                this.gapColour = value;
+            }
+
+            /**
+             * Gets the value of the hiddenColour property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getHiddenColour() {
+                return hiddenColour;
+            }
+
+            /**
+             * Sets the value of the hiddenColour property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setHiddenColour(Integer value) {
+                this.hiddenColour = value;
+            }
+
+            /**
+             * Gets the value of the title property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getTitle() {
+                return title;
+            }
+
+            /**
+             * Sets the value of the title property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setTitle(String value) {
+                this.title = value;
+            }
+
+            /**
+             * Gets the value of the width property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getWidth() {
+                return width;
+            }
+
+            /**
+             * Sets the value of the width property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setWidth(Integer value) {
+                this.width = value;
+            }
+
+            /**
+             * Gets the value of the height property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getHeight() {
+                return height;
+            }
+
+            /**
+             * Sets the value of the height property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setHeight(Integer value) {
+                this.height = value;
+            }
+
+            /**
+             * Gets the value of the xpos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getXpos() {
+                return xpos;
+            }
+
+            /**
+             * Sets the value of the xpos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setXpos(Integer value) {
+                this.xpos = value;
+            }
+
+            /**
+             * Gets the value of the ypos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getYpos() {
+                return ypos;
+            }
+
+            /**
+             * Sets the value of the ypos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setYpos(Integer value) {
+                this.ypos = value;
+            }
 
-    }
+        }
 
-  }
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/JalviewModelType.java b/src/jalview/xml/binding/jalview/JalviewModelType.java
deleted file mode 100644
index 0541d7a..0000000
--- a/src/jalview/xml/binding/jalview/JalviewModelType.java
+++ /dev/null
@@ -1,5233 +0,0 @@
-//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
-// Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2018.09.18 at 01:33:02 PM BST 
-//
-
-package jalview.xml.binding.jalview;
-
-import java.util.ArrayList;
-import java.util.List;
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlID;
-import javax.xml.bind.annotation.XmlSchemaType;
-import javax.xml.bind.annotation.XmlType;
-import javax.xml.bind.annotation.XmlValue;
-import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
-import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
-import javax.xml.datatype.XMLGregorianCalendar;
-
-/**
- * <p>
- * Java class for JalviewModelType complex type.
- * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
- * 
- * <pre>
- * &lt;complexType name="JalviewModelType">
- *   &lt;complexContent>
- *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       &lt;sequence>
- *         &lt;element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
- *         &lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
- *         &lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
- *         &lt;sequence>
- *           &lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0">
- *             &lt;complexType>
- *               &lt;complexContent>
- *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   &lt;sequence>
- *                     &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
- *                     &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;extension base="{www.jalview.org}pdbentry">
- *                             &lt;sequence>
- *                               &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
- *                                 &lt;complexType>
- *                                   &lt;simpleContent>
- *                                     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
- *                                       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
- *                                       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                                       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                                       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                                       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                                       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                     &lt;/extension>
- *                                   &lt;/simpleContent>
- *                                 &lt;/complexType>
- *                               &lt;/element>
- *                             &lt;/sequence>
- *                           &lt;/extension>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                     &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
- *                     &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             &lt;sequence>
- *                               &lt;element name="secondaryStructure" maxOccurs="unbounded">
- *                                 &lt;complexType>
- *                                   &lt;complexContent>
- *                                     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                                       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                                       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                     &lt;/restriction>
- *                                   &lt;/complexContent>
- *                                 &lt;/complexType>
- *                               &lt;/element>
- *                             &lt;/sequence>
- *                             &lt;attGroup ref="{www.jalview.org}swingwindow"/>
- *                             &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                           &lt;/restriction>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                   &lt;/sequence>
- *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                 &lt;/restriction>
- *               &lt;/complexContent>
- *             &lt;/complexType>
- *           &lt;/element>
- *           &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0">
- *             &lt;complexType>
- *               &lt;complexContent>
- *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   &lt;sequence>
- *                     &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
- *                     &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- *                   &lt;/sequence>
- *                   &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 &lt;/restriction>
- *               &lt;/complexContent>
- *             &lt;/complexType>
- *           &lt;/element>
- *           &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0">
- *             &lt;complexType>
- *               &lt;complexContent>
- *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   &lt;sequence>
- *                     &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- *                     &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                           &lt;/restriction>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                     &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
- *                             &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                             &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                           &lt;/extension>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                   &lt;/sequence>
- *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
- *                   &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- *                   &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 &lt;/restriction>
- *               &lt;/complexContent>
- *             &lt;/complexType>
- *           &lt;/element>
- *           &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0">
- *             &lt;complexType>
- *               &lt;complexContent>
- *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   &lt;sequence>
- *                     &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
- *                   &lt;/sequence>
- *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 &lt;/restriction>
- *               &lt;/complexContent>
- *             &lt;/complexType>
- *           &lt;/element>
- *           &lt;element name="tree" maxOccurs="unbounded" minOccurs="0">
- *             &lt;complexType>
- *               &lt;complexContent>
- *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   &lt;sequence minOccurs="0">
- *                     &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
- *                     &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
- *                   &lt;/sequence>
- *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
- *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                   &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- *                 &lt;/restriction>
- *               &lt;/complexContent>
- *             &lt;/complexType>
- *           &lt;/element>
- *           &lt;element name="FeatureSettings" minOccurs="0">
- *             &lt;complexType>
- *               &lt;complexContent>
- *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   &lt;sequence>
- *                     &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             &lt;sequence>
- *                               &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- *                               &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
- *                             &lt;/sequence>
- *                             &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                             &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                             &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- *                             &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                             &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                             &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                             &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                             &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                           &lt;/restriction>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                     &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                           &lt;/restriction>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                   &lt;/sequence>
- *                 &lt;/restriction>
- *               &lt;/complexContent>
- *             &lt;/complexType>
- *           &lt;/element>
- *         &lt;/sequence>
- *       &lt;/sequence>
- *     &lt;/restriction>
- *   &lt;/complexContent>
- * &lt;/complexType>
- * </pre>
- * 
- * 
- */
-@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "JalviewModelType",
-  namespace = "www.jalview.org",
-  propOrder =
-  { "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport",
-      "userColours", "tree", "featureSettings" })
-public class JalviewModelType
-{
-
-  @XmlElement(required = true)
-  @XmlSchemaType(name = "dateTime")
-  protected XMLGregorianCalendar creationDate;
-
-  @XmlElement(required = true)
-  protected String version;
-
-  @XmlElement(required = true)
-  protected VAMSAS vamsasModel;
-
-  @XmlElement(name = "JSeq")
-  protected List<JalviewModelType.JSeq> jSeq;
-
-  @XmlElement(name = "JGroup")
-  protected List<JalviewModelType.JGroup> jGroup;
-
-  @XmlElement(name = "Viewport")
-  protected List<JalviewModelType.Viewport> viewport;
-
-  @XmlElement(name = "UserColours")
-  protected List<JalviewModelType.UserColours> userColours;
-
-  protected List<JalviewModelType.Tree> tree;
-
-  @XmlElement(name = "FeatureSettings")
-  protected JalviewModelType.FeatureSettings featureSettings;
-
-  /**
-   * Gets the value of the creationDate property.
-   * 
-   * @return possible object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public XMLGregorianCalendar getCreationDate()
-  {
-    return creationDate;
-  }
-
-  /**
-   * Sets the value of the creationDate property.
-   * 
-   * @param value
-   *          allowed object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public void setCreationDate(XMLGregorianCalendar value)
-  {
-    this.creationDate = value;
-  }
-
-  /**
-   * Gets the value of the version property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getVersion()
-  {
-    return version;
-  }
-
-  /**
-   * Sets the value of the version property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setVersion(String value)
-  {
-    this.version = value;
-  }
-
-  /**
-   * Gets the value of the vamsasModel property.
-   * 
-   * @return possible object is {@link VAMSAS }
-   * 
-   */
-  public VAMSAS getVamsasModel()
-  {
-    return vamsasModel;
-  }
-
-  /**
-   * Sets the value of the vamsasModel property.
-   * 
-   * @param value
-   *          allowed object is {@link VAMSAS }
-   * 
-   */
-  public void setVamsasModel(VAMSAS value)
-  {
-    this.vamsasModel = value;
-  }
-
-  /**
-   * Gets the value of the jSeq property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the jSeq property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getJSeq().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link JalviewModelType.JSeq }
-   * 
-   * 
-   */
-  public List<JalviewModelType.JSeq> getJSeq()
-  {
-    if (jSeq == null)
-    {
-      jSeq = new ArrayList<JalviewModelType.JSeq>();
-    }
-    return this.jSeq;
-  }
-
-  /**
-   * Gets the value of the jGroup property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the jGroup property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getJGroup().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link JalviewModelType.JGroup }
-   * 
-   * 
-   */
-  public List<JalviewModelType.JGroup> getJGroup()
-  {
-    if (jGroup == null)
-    {
-      jGroup = new ArrayList<JalviewModelType.JGroup>();
-    }
-    return this.jGroup;
-  }
-
-  /**
-   * Gets the value of the viewport property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the viewport property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getViewport().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link JalviewModelType.Viewport }
-   * 
-   * 
-   */
-  public List<JalviewModelType.Viewport> getViewport()
-  {
-    if (viewport == null)
-    {
-      viewport = new ArrayList<JalviewModelType.Viewport>();
-    }
-    return this.viewport;
-  }
-
-  /**
-   * Gets the value of the userColours property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the userColours property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getUserColours().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link JalviewModelType.UserColours }
-   * 
-   * 
-   */
-  public List<JalviewModelType.UserColours> getUserColours()
-  {
-    if (userColours == null)
-    {
-      userColours = new ArrayList<JalviewModelType.UserColours>();
-    }
-    return this.userColours;
-  }
-
-  /**
-   * Gets the value of the tree property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the tree property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getTree().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link JalviewModelType.Tree }
-   * 
-   * 
-   */
-  public List<JalviewModelType.Tree> getTree()
-  {
-    if (tree == null)
-    {
-      tree = new ArrayList<JalviewModelType.Tree>();
-    }
-    return this.tree;
-  }
-
-  /**
-   * Gets the value of the featureSettings property.
-   * 
-   * @return possible object is {@link JalviewModelType.FeatureSettings }
-   * 
-   */
-  public JalviewModelType.FeatureSettings getFeatureSettings()
-  {
-    return featureSettings;
-  }
-
-  /**
-   * Sets the value of the featureSettings property.
-   * 
-   * @param value
-   *          allowed object is {@link JalviewModelType.FeatureSettings }
-   * 
-   */
-  public void setFeatureSettings(JalviewModelType.FeatureSettings value)
-  {
-    this.featureSettings = value;
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;sequence>
-   *         &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
-   *           &lt;complexType>
-   *             &lt;complexContent>
-   *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 &lt;sequence>
-   *                   &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
-   *                   &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
-   *                 &lt;/sequence>
-   *                 &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *                 &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
-   *                 &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *                 &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
-   *                 &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-   *                 &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *                 &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
-   *                 &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
-   *                 &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *                 &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *               &lt;/restriction>
-   *             &lt;/complexContent>
-   *           &lt;/complexType>
-   *         &lt;/element>
-   *         &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
-   *           &lt;complexType>
-   *             &lt;complexContent>
-   *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *               &lt;/restriction>
-   *             &lt;/complexContent>
-   *           &lt;/complexType>
-   *         &lt;/element>
-   *       &lt;/sequence>
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "setting", "group" })
-  public static class FeatureSettings
-  {
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List<JalviewModelType.FeatureSettings.Setting> setting;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List<JalviewModelType.FeatureSettings.Group> group;
-
-    /**
-     * Gets the value of the setting property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the setting property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * 
-     * <pre>
-     * getSetting().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModelType.FeatureSettings.Setting }
-     * 
-     * 
-     */
-    public List<JalviewModelType.FeatureSettings.Setting> getSetting()
-    {
-      if (setting == null)
-      {
-        setting = new ArrayList<JalviewModelType.FeatureSettings.Setting>();
-      }
-      return this.setting;
-    }
-
-    /**
-     * Gets the value of the group property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the group property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * 
-     * <pre>
-     * getGroup().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModelType.FeatureSettings.Group }
-     * 
-     * 
-     */
-    public List<JalviewModelType.FeatureSettings.Group> getGroup()
-    {
-      if (group == null)
-      {
-        group = new ArrayList<JalviewModelType.FeatureSettings.Group>();
-      }
-      return this.group;
-    }
-
-    /**
-     * <p>
-     * Java class for anonymous complex type.
-     * 
-     * <p>
-     * The following schema fragment specifies the expected content contained
-     * within this class.
-     * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class Group
-    {
-
-      @XmlAttribute(name = "name", required = true)
-      protected String name;
-
-      @XmlAttribute(name = "display", required = true)
-      protected boolean display;
-
-      /**
-       * Gets the value of the name property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getName()
-      {
-        return name;
-      }
-
-      /**
-       * Sets the value of the name property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setName(String value)
-      {
-        this.name = value;
-      }
-
-      /**
-       * Gets the value of the display property.
-       * 
-       */
-      public boolean isDisplay()
-      {
-        return display;
-      }
-
-      /**
-       * Sets the value of the display property.
-       * 
-       */
-      public void setDisplay(boolean value)
-      {
-        this.display = value;
-      }
-
-    }
-
-    /**
-     * <p>
-     * Java class for anonymous complex type.
-     * 
-     * <p>
-     * The following schema fragment specifies the expected content contained
-     * within this class.
-     * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
-     *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
-     *       &lt;/sequence>
-     *       &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
-     *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = { "attributeName", "matcherSet" })
-    public static class Setting
-    {
-
-      @XmlElement(namespace = "www.jalview.org")
-      protected List<String> attributeName;
-
-      @XmlElement(namespace = "www.jalview.org")
-      protected FeatureMatcherSet matcherSet;
-
-      @XmlAttribute(name = "type", required = true)
-      protected String type;
-
-      @XmlAttribute(name = "colour", required = true)
-      protected int colour;
-
-      @XmlAttribute(name = "display", required = true)
-      protected boolean display;
-
-      @XmlAttribute(name = "order")
-      protected Float order;
-
-      @XmlAttribute(name = "mincolour")
-      protected Integer mincolour;
-
-      @XmlAttribute(name = "noValueColour")
-      protected NoValueColour noValueColour;
-
-      @XmlAttribute(name = "threshold")
-      protected Float threshold;
-
-      @XmlAttribute(name = "threshstate")
-      protected Integer threshstate;
-
-      @XmlAttribute(name = "max")
-      protected Float max;
-
-      @XmlAttribute(name = "min")
-      protected Float min;
-
-      @XmlAttribute(name = "colourByLabel")
-      protected Boolean colourByLabel;
-
-      @XmlAttribute(name = "autoScale")
-      protected Boolean autoScale;
-
-      /**
-       * Gets the value of the attributeName property.
-       * 
-       * <p>
-       * This accessor method returns a reference to the live list, not a
-       * snapshot. Therefore any modification you make to the returned list will
-       * be present inside the JAXB object. This is why there is not a
-       * <CODE>set</CODE> method for the attributeName property.
-       * 
-       * <p>
-       * For example, to add a new item, do as follows:
-       * 
-       * <pre>
-       * getAttributeName().add(newItem);
-       * </pre>
-       * 
-       * 
-       * <p>
-       * Objects of the following type(s) are allowed in the list {@link String
-       * }
-       * 
-       * 
-       */
-      public List<String> getAttributeName()
-      {
-        if (attributeName == null)
-        {
-          attributeName = new ArrayList<String>();
-        }
-        return this.attributeName;
-      }
-
-      /**
-       * Gets the value of the matcherSet property.
-       * 
-       * @return possible object is {@link FeatureMatcherSet }
-       * 
-       */
-      public FeatureMatcherSet getMatcherSet()
-      {
-        return matcherSet;
-      }
-
-      /**
-       * Sets the value of the matcherSet property.
-       * 
-       * @param value
-       *          allowed object is {@link FeatureMatcherSet }
-       * 
-       */
-      public void setMatcherSet(FeatureMatcherSet value)
-      {
-        this.matcherSet = value;
-      }
-
-      /**
-       * Gets the value of the type property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getType()
-      {
-        return type;
-      }
-
-      /**
-       * Sets the value of the type property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setType(String value)
-      {
-        this.type = value;
-      }
-
-      /**
-       * Gets the value of the colour property.
-       * 
-       */
-      public int getColour()
-      {
-        return colour;
-      }
-
-      /**
-       * Sets the value of the colour property.
-       * 
-       */
-      public void setColour(int value)
-      {
-        this.colour = value;
-      }
-
-      /**
-       * Gets the value of the display property.
-       * 
-       */
-      public boolean isDisplay()
-      {
-        return display;
-      }
-
-      /**
-       * Sets the value of the display property.
-       * 
-       */
-      public void setDisplay(boolean value)
-      {
-        this.display = value;
-      }
-
-      /**
-       * Gets the value of the order property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getOrder()
-      {
-        return order;
-      }
-
-      /**
-       * Sets the value of the order property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setOrder(Float value)
-      {
-        this.order = value;
-      }
-
-      /**
-       * Gets the value of the mincolour property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getMincolour()
-      {
-        return mincolour;
-      }
-
-      /**
-       * Sets the value of the mincolour property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setMincolour(Integer value)
-      {
-        this.mincolour = value;
-      }
-
-      /**
-       * Gets the value of the noValueColour property.
-       * 
-       * @return possible object is {@link NoValueColour }
-       * 
-       */
-      public NoValueColour getNoValueColour()
-      {
-        if (noValueColour == null)
-        {
-          return NoValueColour.MIN;
-        }
-        else
-        {
-          return noValueColour;
-        }
-      }
-
-      /**
-       * Sets the value of the noValueColour property.
-       * 
-       * @param value
-       *          allowed object is {@link NoValueColour }
-       * 
-       */
-      public void setNoValueColour(NoValueColour value)
-      {
-        this.noValueColour = value;
-      }
-
-      /**
-       * Gets the value of the threshold property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getThreshold()
-      {
-        return threshold;
-      }
-
-      /**
-       * Sets the value of the threshold property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setThreshold(Float value)
-      {
-        this.threshold = value;
-      }
-
-      /**
-       * Gets the value of the threshstate property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getThreshstate()
-      {
-        return threshstate;
-      }
-
-      /**
-       * Sets the value of the threshstate property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setThreshstate(Integer value)
-      {
-        this.threshstate = value;
-      }
-
-      /**
-       * Gets the value of the max property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getMax()
-      {
-        return max;
-      }
-
-      /**
-       * Sets the value of the max property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setMax(Float value)
-      {
-        this.max = value;
-      }
-
-      /**
-       * Gets the value of the min property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getMin()
-      {
-        return min;
-      }
-
-      /**
-       * Sets the value of the min property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setMin(Float value)
-      {
-        this.min = value;
-      }
-
-      /**
-       * Gets the value of the colourByLabel property.
-       * 
-       * @return possible object is {@link Boolean }
-       * 
-       */
-      public Boolean isColourByLabel()
-      {
-        return colourByLabel;
-      }
-
-      /**
-       * Sets the value of the colourByLabel property.
-       * 
-       * @param value
-       *          allowed object is {@link Boolean }
-       * 
-       */
-      public void setColourByLabel(Boolean value)
-      {
-        this.colourByLabel = value;
-      }
-
-      /**
-       * Gets the value of the autoScale property.
-       * 
-       * @return possible object is {@link Boolean }
-       * 
-       */
-      public Boolean isAutoScale()
-      {
-        return autoScale;
-      }
-
-      /**
-       * Sets the value of the autoScale property.
-       * 
-       * @param value
-       *          allowed object is {@link Boolean }
-       * 
-       */
-      public void setAutoScale(Boolean value)
-      {
-        this.autoScale = value;
-      }
-
-    }
-
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;sequence>
-   *         &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
-   *         &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
-   *       &lt;/sequence>
-   *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "seq", "annotationColours" })
-  public static class JGroup
-  {
-
-    @XmlElement(namespace = "www.jalview.org", required = true)
-    protected List<String> seq;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected AnnotationColourScheme annotationColours;
-
-    @XmlAttribute(name = "start")
-    protected Integer start;
-
-    @XmlAttribute(name = "end")
-    protected Integer end;
-
-    @XmlAttribute(name = "name")
-    protected String name;
-
-    @XmlAttribute(name = "colour")
-    protected String colour;
-
-    @XmlAttribute(name = "consThreshold")
-    protected Integer consThreshold;
-
-    @XmlAttribute(name = "pidThreshold")
-    protected Integer pidThreshold;
-
-    @XmlAttribute(name = "outlineColour")
-    protected Integer outlineColour;
-
-    @XmlAttribute(name = "displayBoxes")
-    protected Boolean displayBoxes;
-
-    @XmlAttribute(name = "displayText")
-    protected Boolean displayText;
-
-    @XmlAttribute(name = "colourText")
-    protected Boolean colourText;
-
-    @XmlAttribute(name = "textCol1")
-    protected Integer textCol1;
-
-    @XmlAttribute(name = "textCol2")
-    protected Integer textCol2;
-
-    @XmlAttribute(name = "textColThreshold")
-    protected Integer textColThreshold;
-
-    @XmlAttribute(name = "showUnconserved")
-    protected Boolean showUnconserved;
-
-    @XmlAttribute(name = "ignoreGapsinConsensus")
-    protected Boolean ignoreGapsinConsensus;
-
-    @XmlAttribute(name = "showConsensusHistogram")
-    protected Boolean showConsensusHistogram;
-
-    @XmlAttribute(name = "showSequenceLogo")
-    protected Boolean showSequenceLogo;
-
-    @XmlAttribute(name = "normaliseSequenceLogo")
-    protected Boolean normaliseSequenceLogo;
-
-    @XmlAttribute(name = "id")
-    protected String id;
-
-    /**
-     * Gets the value of the seq property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the seq property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * 
-     * <pre>
-     * getSeq().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list {@link String }
-     * 
-     * 
-     */
-    public List<String> getSeq()
-    {
-      if (seq == null)
-      {
-        seq = new ArrayList<String>();
-      }
-      return this.seq;
-    }
-
-    /**
-     * Gets the value of the annotationColours property.
-     * 
-     * @return possible object is {@link AnnotationColourScheme }
-     * 
-     */
-    public AnnotationColourScheme getAnnotationColours()
-    {
-      return annotationColours;
-    }
-
-    /**
-     * Sets the value of the annotationColours property.
-     * 
-     * @param value
-     *          allowed object is {@link AnnotationColourScheme }
-     * 
-     */
-    public void setAnnotationColours(AnnotationColourScheme value)
-    {
-      this.annotationColours = value;
-    }
-
-    /**
-     * Gets the value of the start property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getStart()
-    {
-      return start;
-    }
-
-    /**
-     * Sets the value of the start property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setStart(Integer value)
-    {
-      this.start = value;
-    }
-
-    /**
-     * Gets the value of the end property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getEnd()
-    {
-      return end;
-    }
-
-    /**
-     * Sets the value of the end property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setEnd(Integer value)
-    {
-      this.end = value;
-    }
-
-    /**
-     * Gets the value of the name property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getName()
-    {
-      return name;
-    }
-
-    /**
-     * Sets the value of the name property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setName(String value)
-    {
-      this.name = value;
-    }
-
-    /**
-     * Gets the value of the colour property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getColour()
-    {
-      return colour;
-    }
-
-    /**
-     * Sets the value of the colour property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setColour(String value)
-    {
-      this.colour = value;
-    }
-
-    /**
-     * Gets the value of the consThreshold property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getConsThreshold()
-    {
-      return consThreshold;
-    }
-
-    /**
-     * Sets the value of the consThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setConsThreshold(Integer value)
-    {
-      this.consThreshold = value;
-    }
-
-    /**
-     * Gets the value of the pidThreshold property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getPidThreshold()
-    {
-      return pidThreshold;
-    }
-
-    /**
-     * Sets the value of the pidThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setPidThreshold(Integer value)
-    {
-      this.pidThreshold = value;
-    }
-
-    /**
-     * Gets the value of the outlineColour property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getOutlineColour()
-    {
-      return outlineColour;
-    }
-
-    /**
-     * Sets the value of the outlineColour property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setOutlineColour(Integer value)
-    {
-      this.outlineColour = value;
-    }
-
-    /**
-     * Gets the value of the displayBoxes property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isDisplayBoxes()
-    {
-      return displayBoxes;
-    }
-
-    /**
-     * Sets the value of the displayBoxes property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setDisplayBoxes(Boolean value)
-    {
-      this.displayBoxes = value;
-    }
-
-    /**
-     * Gets the value of the displayText property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isDisplayText()
-    {
-      return displayText;
-    }
-
-    /**
-     * Sets the value of the displayText property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setDisplayText(Boolean value)
-    {
-      this.displayText = value;
-    }
-
-    /**
-     * Gets the value of the colourText property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isColourText()
-    {
-      return colourText;
-    }
-
-    /**
-     * Sets the value of the colourText property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setColourText(Boolean value)
-    {
-      this.colourText = value;
-    }
-
-    /**
-     * Gets the value of the textCol1 property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getTextCol1()
-    {
-      return textCol1;
-    }
-
-    /**
-     * Sets the value of the textCol1 property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextCol1(Integer value)
-    {
-      this.textCol1 = value;
-    }
-
-    /**
-     * Gets the value of the textCol2 property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getTextCol2()
-    {
-      return textCol2;
-    }
-
-    /**
-     * Sets the value of the textCol2 property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextCol2(Integer value)
-    {
-      this.textCol2 = value;
-    }
-
-    /**
-     * Gets the value of the textColThreshold property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getTextColThreshold()
-    {
-      return textColThreshold;
-    }
-
-    /**
-     * Sets the value of the textColThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextColThreshold(Integer value)
-    {
-      this.textColThreshold = value;
-    }
-
-    /**
-     * Gets the value of the showUnconserved property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowUnconserved()
-    {
-      return showUnconserved;
-    }
-
-    /**
-     * Sets the value of the showUnconserved property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowUnconserved(Boolean value)
-    {
-      this.showUnconserved = value;
-    }
-
-    /**
-     * Gets the value of the ignoreGapsinConsensus property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isIgnoreGapsinConsensus()
-    {
-      if (ignoreGapsinConsensus == null)
-      {
-        return true;
-      }
-      else
-      {
-        return ignoreGapsinConsensus;
-      }
-    }
-
-    /**
-     * Sets the value of the ignoreGapsinConsensus property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setIgnoreGapsinConsensus(Boolean value)
-    {
-      this.ignoreGapsinConsensus = value;
-    }
-
-    /**
-     * Gets the value of the showConsensusHistogram property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowConsensusHistogram()
-    {
-      if (showConsensusHistogram == null)
-      {
-        return true;
-      }
-      else
-      {
-        return showConsensusHistogram;
-      }
-    }
-
-    /**
-     * Sets the value of the showConsensusHistogram property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowConsensusHistogram(Boolean value)
-    {
-      this.showConsensusHistogram = value;
-    }
-
-    /**
-     * Gets the value of the showSequenceLogo property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowSequenceLogo()
-    {
-      if (showSequenceLogo == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showSequenceLogo;
-      }
-    }
-
-    /**
-     * Sets the value of the showSequenceLogo property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowSequenceLogo(Boolean value)
-    {
-      this.showSequenceLogo = value;
-    }
-
-    /**
-     * Gets the value of the normaliseSequenceLogo property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isNormaliseSequenceLogo()
-    {
-      if (normaliseSequenceLogo == null)
-      {
-        return false;
-      }
-      else
-      {
-        return normaliseSequenceLogo;
-      }
-    }
-
-    /**
-     * Sets the value of the normaliseSequenceLogo property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setNormaliseSequenceLogo(Boolean value)
-    {
-      this.normaliseSequenceLogo = value;
-    }
-
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getId()
-    {
-      return id;
-    }
-
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setId(String value)
-    {
-      this.id = value;
-    }
-
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;sequence>
-   *         &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
-   *         &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
-   *           &lt;complexType>
-   *             &lt;complexContent>
-   *               &lt;extension base="{www.jalview.org}pdbentry">
-   *                 &lt;sequence>
-   *                   &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
-   *                     &lt;complexType>
-   *                       &lt;simpleContent>
-   *                         &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
-   *                           &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-   *                           &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *                           &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                           &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *                           &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *                           &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *                           &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                         &lt;/extension>
-   *                       &lt;/simpleContent>
-   *                     &lt;/complexType>
-   *                   &lt;/element>
-   *                 &lt;/sequence>
-   *               &lt;/extension>
-   *             &lt;/complexContent>
-   *           &lt;/complexType>
-   *         &lt;/element>
-   *         &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
-   *         &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
-   *           &lt;complexType>
-   *             &lt;complexContent>
-   *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 &lt;sequence>
-   *                   &lt;element name="secondaryStructure" maxOccurs="unbounded">
-   *                     &lt;complexType>
-   *                       &lt;complexContent>
-   *                         &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                           &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                           &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                           &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *                           &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                         &lt;/restriction>
-   *                       &lt;/complexContent>
-   *                     &lt;/complexType>
-   *                   &lt;/element>
-   *                 &lt;/sequence>
-   *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-   *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *                 &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *               &lt;/restriction>
-   *             &lt;/complexContent>
-   *           &lt;/complexType>
-   *         &lt;/element>
-   *       &lt;/sequence>
-   *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(
-    name = "",
-    propOrder =
-    { "features", "pdbids", "hiddenSequences", "rnaViewer" })
-  public static class JSeq
-  {
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List<Feature> features;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List<JalviewModelType.JSeq.Pdbids> pdbids;
-
-    @XmlElement(namespace = "www.jalview.org", type = Integer.class)
-    protected List<Integer> hiddenSequences;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List<JalviewModelType.JSeq.RnaViewer> rnaViewer;
-
-    @XmlAttribute(name = "colour")
-    protected Integer colour;
-
-    @XmlAttribute(name = "start", required = true)
-    protected int start;
-
-    @XmlAttribute(name = "end", required = true)
-    protected int end;
-
-    @XmlAttribute(name = "id", required = true)
-    protected String id;
-
-    @XmlAttribute(name = "hidden")
-    protected Boolean hidden;
-
-    @XmlAttribute(name = "viewreference")
-    protected Boolean viewreference;
-
-    /**
-     * Gets the value of the features property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the features property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * 
-     * <pre>
-     * getFeatures().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list {@link Feature }
-     * 
-     * 
-     */
-    public List<Feature> getFeatures()
-    {
-      if (features == null)
-      {
-        features = new ArrayList<Feature>();
-      }
-      return this.features;
-    }
-
-    /**
-     * Gets the value of the pdbids property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the pdbids property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * 
-     * <pre>
-     * getPdbids().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModelType.JSeq.Pdbids }
-     * 
-     * 
-     */
-    public List<JalviewModelType.JSeq.Pdbids> getPdbids()
-    {
-      if (pdbids == null)
-      {
-        pdbids = new ArrayList<JalviewModelType.JSeq.Pdbids>();
-      }
-      return this.pdbids;
-    }
-
-    /**
-     * Gets the value of the hiddenSequences property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the hiddenSequences property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * 
-     * <pre>
-     * getHiddenSequences().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list {@link Integer }
-     * 
-     * 
-     */
-    public List<Integer> getHiddenSequences()
-    {
-      if (hiddenSequences == null)
-      {
-        hiddenSequences = new ArrayList<Integer>();
-      }
-      return this.hiddenSequences;
-    }
-
-    /**
-     * Gets the value of the rnaViewer property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the rnaViewer property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * 
-     * <pre>
-     * getRnaViewer().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModelType.JSeq.RnaViewer }
-     * 
-     * 
-     */
-    public List<JalviewModelType.JSeq.RnaViewer> getRnaViewer()
-    {
-      if (rnaViewer == null)
-      {
-        rnaViewer = new ArrayList<JalviewModelType.JSeq.RnaViewer>();
-      }
-      return this.rnaViewer;
-    }
-
-    /**
-     * Gets the value of the colour property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getColour()
-    {
-      return colour;
-    }
-
-    /**
-     * Sets the value of the colour property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setColour(Integer value)
-    {
-      this.colour = value;
-    }
-
-    /**
-     * Gets the value of the start property.
-     * 
-     */
-    public int getStart()
-    {
-      return start;
-    }
-
-    /**
-     * Sets the value of the start property.
-     * 
-     */
-    public void setStart(int value)
-    {
-      this.start = value;
-    }
-
-    /**
-     * Gets the value of the end property.
-     * 
-     */
-    public int getEnd()
-    {
-      return end;
-    }
-
-    /**
-     * Sets the value of the end property.
-     * 
-     */
-    public void setEnd(int value)
-    {
-      this.end = value;
-    }
-
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getId()
-    {
-      return id;
-    }
-
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setId(String value)
-    {
-      this.id = value;
-    }
-
-    /**
-     * Gets the value of the hidden property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isHidden()
-    {
-      return hidden;
-    }
-
-    /**
-     * Sets the value of the hidden property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setHidden(Boolean value)
-    {
-      this.hidden = value;
-    }
-
-    /**
-     * Gets the value of the viewreference property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isViewreference()
-    {
-      return viewreference;
-    }
-
-    /**
-     * Sets the value of the viewreference property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setViewreference(Boolean value)
-    {
-      this.viewreference = value;
-    }
-
-    /**
-     * <p>
-     * Java class for anonymous complex type.
-     * 
-     * <p>
-     * The following schema fragment specifies the expected content contained
-     * within this class.
-     * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;extension base="{www.jalview.org}pdbentry">
-     *       &lt;sequence>
-     *         &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
-     *           &lt;complexType>
-     *             &lt;simpleContent>
-     *               &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
-     *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-     *                 &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *                 &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *                 &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *                 &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *               &lt;/extension>
-     *             &lt;/simpleContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *       &lt;/sequence>
-     *     &lt;/extension>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = { "structureState" })
-    public static class Pdbids extends Pdbentry
-    {
-
-      @XmlElement(namespace = "www.jalview.org")
-      protected List<JalviewModelType.JSeq.Pdbids.StructureState> structureState;
-
-      /**
-       * Gets the value of the structureState property.
-       * 
-       * <p>
-       * This accessor method returns a reference to the live list, not a
-       * snapshot. Therefore any modification you make to the returned list will
-       * be present inside the JAXB object. This is why there is not a
-       * <CODE>set</CODE> method for the structureState property.
-       * 
-       * <p>
-       * For example, to add a new item, do as follows:
-       * 
-       * <pre>
-       * getStructureState().add(newItem);
-       * </pre>
-       * 
-       * 
-       * <p>
-       * Objects of the following type(s) are allowed in the list
-       * {@link JalviewModelType.JSeq.Pdbids.StructureState }
-       * 
-       * 
-       */
-      public List<JalviewModelType.JSeq.Pdbids.StructureState> getStructureState()
-      {
-        if (structureState == null)
-        {
-          structureState = new ArrayList<JalviewModelType.JSeq.Pdbids.StructureState>();
-        }
-        return this.structureState;
-      }
-
-      /**
-       * <p>
-       * Java class for anonymous complex type.
-       * 
-       * <p>
-       * The following schema fragment specifies the expected content contained
-       * within this class.
-       * 
-       * <pre>
-       * &lt;complexType>
-       *   &lt;simpleContent>
-       *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
-       *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-       *       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-       *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-       *       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-       *       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-       *       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *     &lt;/extension>
-       *   &lt;/simpleContent>
-       * &lt;/complexType>
-       * </pre>
-       * 
-       * 
-       */
-      @XmlAccessorType(XmlAccessType.FIELD)
-      @XmlType(name = "", propOrder = { "value" })
-      public static class StructureState
-      {
-
-        @XmlValue
-        protected String value;
-
-        @XmlAttribute(name = "visible")
-        protected Boolean visible;
-
-        @XmlAttribute(name = "viewId")
-        protected String viewId;
-
-        @XmlAttribute(name = "alignwithAlignPanel")
-        protected Boolean alignwithAlignPanel;
-
-        @XmlAttribute(name = "colourwithAlignPanel")
-        protected Boolean colourwithAlignPanel;
-
-        @XmlAttribute(name = "colourByJmol")
-        protected Boolean colourByJmol;
-
-        @XmlAttribute(name = "type")
-        protected String type;
-
-        @XmlAttribute(name = "width")
-        protected Integer width;
-
-        @XmlAttribute(name = "height")
-        protected Integer height;
-
-        @XmlAttribute(name = "xpos")
-        protected Integer xpos;
-
-        @XmlAttribute(name = "ypos")
-        protected Integer ypos;
-
-        /**
-         * Gets the value of the value property.
-         * 
-         * @return possible object is {@link String }
-         * 
-         */
-        public String getValue()
-        {
-          return value;
-        }
-
-        /**
-         * Sets the value of the value property.
-         * 
-         * @param value
-         *          allowed object is {@link String }
-         * 
-         */
-        public void setValue(String value)
-        {
-          this.value = value;
-        }
-
-        /**
-         * Gets the value of the visible property.
-         * 
-         * @return possible object is {@link Boolean }
-         * 
-         */
-        public Boolean isVisible()
-        {
-          return visible;
-        }
-
-        /**
-         * Sets the value of the visible property.
-         * 
-         * @param value
-         *          allowed object is {@link Boolean }
-         * 
-         */
-        public void setVisible(Boolean value)
-        {
-          this.visible = value;
-        }
-
-        /**
-         * Gets the value of the viewId property.
-         * 
-         * @return possible object is {@link String }
-         * 
-         */
-        public String getViewId()
-        {
-          return viewId;
-        }
-
-        /**
-         * Sets the value of the viewId property.
-         * 
-         * @param value
-         *          allowed object is {@link String }
-         * 
-         */
-        public void setViewId(String value)
-        {
-          this.viewId = value;
-        }
-
-        /**
-         * Gets the value of the alignwithAlignPanel property.
-         * 
-         * @return possible object is {@link Boolean }
-         * 
-         */
-        public boolean isAlignwithAlignPanel()
-        {
-          if (alignwithAlignPanel == null)
-          {
-            return true;
-          }
-          else
-          {
-            return alignwithAlignPanel;
-          }
-        }
-
-        /**
-         * Sets the value of the alignwithAlignPanel property.
-         * 
-         * @param value
-         *          allowed object is {@link Boolean }
-         * 
-         */
-        public void setAlignwithAlignPanel(Boolean value)
-        {
-          this.alignwithAlignPanel = value;
-        }
-
-        /**
-         * Gets the value of the colourwithAlignPanel property.
-         * 
-         * @return possible object is {@link Boolean }
-         * 
-         */
-        public boolean isColourwithAlignPanel()
-        {
-          if (colourwithAlignPanel == null)
-          {
-            return false;
-          }
-          else
-          {
-            return colourwithAlignPanel;
-          }
-        }
-
-        /**
-         * Sets the value of the colourwithAlignPanel property.
-         * 
-         * @param value
-         *          allowed object is {@link Boolean }
-         * 
-         */
-        public void setColourwithAlignPanel(Boolean value)
-        {
-          this.colourwithAlignPanel = value;
-        }
-
-        /**
-         * Gets the value of the colourByJmol property.
-         * 
-         * @return possible object is {@link Boolean }
-         * 
-         */
-        public boolean isColourByJmol()
-        {
-          if (colourByJmol == null)
-          {
-            return true;
-          }
-          else
-          {
-            return colourByJmol;
-          }
-        }
-
-        /**
-         * Sets the value of the colourByJmol property.
-         * 
-         * @param value
-         *          allowed object is {@link Boolean }
-         * 
-         */
-        public void setColourByJmol(Boolean value)
-        {
-          this.colourByJmol = value;
-        }
-
-        /**
-         * Gets the value of the type property.
-         * 
-         * @return possible object is {@link String }
-         * 
-         */
-        public String getType()
-        {
-          return type;
-        }
-
-        /**
-         * Sets the value of the type property.
-         * 
-         * @param value
-         *          allowed object is {@link String }
-         * 
-         */
-        public void setType(String value)
-        {
-          this.type = value;
-        }
-
-        /**
-         * Gets the value of the width property.
-         * 
-         * @return possible object is {@link Integer }
-         * 
-         */
-        public Integer getWidth()
-        {
-          return width;
-        }
-
-        /**
-         * Sets the value of the width property.
-         * 
-         * @param value
-         *          allowed object is {@link Integer }
-         * 
-         */
-        public void setWidth(Integer value)
-        {
-          this.width = value;
-        }
-
-        /**
-         * Gets the value of the height property.
-         * 
-         * @return possible object is {@link Integer }
-         * 
-         */
-        public Integer getHeight()
-        {
-          return height;
-        }
-
-        /**
-         * Sets the value of the height property.
-         * 
-         * @param value
-         *          allowed object is {@link Integer }
-         * 
-         */
-        public void setHeight(Integer value)
-        {
-          this.height = value;
-        }
-
-        /**
-         * Gets the value of the xpos property.
-         * 
-         * @return possible object is {@link Integer }
-         * 
-         */
-        public Integer getXpos()
-        {
-          return xpos;
-        }
-
-        /**
-         * Sets the value of the xpos property.
-         * 
-         * @param value
-         *          allowed object is {@link Integer }
-         * 
-         */
-        public void setXpos(Integer value)
-        {
-          this.xpos = value;
-        }
-
-        /**
-         * Gets the value of the ypos property.
-         * 
-         * @return possible object is {@link Integer }
-         * 
-         */
-        public Integer getYpos()
-        {
-          return ypos;
-        }
-
-        /**
-         * Sets the value of the ypos property.
-         * 
-         * @param value
-         *          allowed object is {@link Integer }
-         * 
-         */
-        public void setYpos(Integer value)
-        {
-          this.ypos = value;
-        }
-
-      }
-
-    }
-
-    /**
-     * <p>
-     * Java class for anonymous complex type.
-     * 
-     * <p>
-     * The following schema fragment specifies the expected content contained
-     * within this class.
-     * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="secondaryStructure" maxOccurs="unbounded">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                 &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *       &lt;/sequence>
-     *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-     *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = { "secondaryStructure" })
-    public static class RnaViewer
-    {
-
-      @XmlElement(namespace = "www.jalview.org", required = true)
-      protected List<JalviewModelType.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
-
-      @XmlAttribute(name = "title")
-      protected String title;
-
-      @XmlAttribute(name = "viewId")
-      protected String viewId;
-
-      @XmlAttribute(name = "dividerLocation")
-      protected Integer dividerLocation;
-
-      @XmlAttribute(name = "selectedRna")
-      protected Integer selectedRna;
-
-      @XmlAttribute(name = "width")
-      protected Integer width;
-
-      @XmlAttribute(name = "height")
-      protected Integer height;
-
-      @XmlAttribute(name = "xpos")
-      protected Integer xpos;
-
-      @XmlAttribute(name = "ypos")
-      protected Integer ypos;
-
-      /**
-       * Gets the value of the secondaryStructure property.
-       * 
-       * <p>
-       * This accessor method returns a reference to the live list, not a
-       * snapshot. Therefore any modification you make to the returned list will
-       * be present inside the JAXB object. This is why there is not a
-       * <CODE>set</CODE> method for the secondaryStructure property.
-       * 
-       * <p>
-       * For example, to add a new item, do as follows:
-       * 
-       * <pre>
-       * getSecondaryStructure().add(newItem);
-       * </pre>
-       * 
-       * 
-       * <p>
-       * Objects of the following type(s) are allowed in the list
-       * {@link JalviewModelType.JSeq.RnaViewer.SecondaryStructure }
-       * 
-       * 
-       */
-      public List<JalviewModelType.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure()
-      {
-        if (secondaryStructure == null)
-        {
-          secondaryStructure = new ArrayList<JalviewModelType.JSeq.RnaViewer.SecondaryStructure>();
-        }
-        return this.secondaryStructure;
-      }
-
-      /**
-       * Gets the value of the title property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getTitle()
-      {
-        return title;
-      }
-
-      /**
-       * Sets the value of the title property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setTitle(String value)
-      {
-        this.title = value;
-      }
-
-      /**
-       * Gets the value of the viewId property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getViewId()
-      {
-        return viewId;
-      }
-
-      /**
-       * Sets the value of the viewId property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setViewId(String value)
-      {
-        this.viewId = value;
-      }
-
-      /**
-       * Gets the value of the dividerLocation property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getDividerLocation()
-      {
-        return dividerLocation;
-      }
-
-      /**
-       * Sets the value of the dividerLocation property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setDividerLocation(Integer value)
-      {
-        this.dividerLocation = value;
-      }
-
-      /**
-       * Gets the value of the selectedRna property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getSelectedRna()
-      {
-        return selectedRna;
-      }
-
-      /**
-       * Sets the value of the selectedRna property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setSelectedRna(Integer value)
-      {
-        this.selectedRna = value;
-      }
-
-      /**
-       * Gets the value of the width property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getWidth()
-      {
-        return width;
-      }
-
-      /**
-       * Sets the value of the width property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setWidth(Integer value)
-      {
-        this.width = value;
-      }
-
-      /**
-       * Gets the value of the height property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getHeight()
-      {
-        return height;
-      }
-
-      /**
-       * Sets the value of the height property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setHeight(Integer value)
-      {
-        this.height = value;
-      }
-
-      /**
-       * Gets the value of the xpos property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getXpos()
-      {
-        return xpos;
-      }
-
-      /**
-       * Sets the value of the xpos property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setXpos(Integer value)
-      {
-        this.xpos = value;
-      }
-
-      /**
-       * Gets the value of the ypos property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getYpos()
-      {
-        return ypos;
-      }
-
-      /**
-       * Sets the value of the ypos property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setYpos(Integer value)
-      {
-        this.ypos = value;
-      }
-
-      /**
-       * <p>
-       * Java class for anonymous complex type.
-       * 
-       * <p>
-       * The following schema fragment specifies the expected content contained
-       * within this class.
-       * 
-       * <pre>
-       * &lt;complexType>
-       *   &lt;complexContent>
-       *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-       *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-       *       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *     &lt;/restriction>
-       *   &lt;/complexContent>
-       * &lt;/complexType>
-       * </pre>
-       * 
-       * 
-       */
-      @XmlAccessorType(XmlAccessType.FIELD)
-      @XmlType(name = "")
-      public static class SecondaryStructure
-      {
-
-        @XmlAttribute(name = "title")
-        protected String title;
-
-        @XmlAttribute(name = "annotationId", required = true)
-        protected String annotationId;
-
-        @XmlAttribute(name = "gapped")
-        protected Boolean gapped;
-
-        @XmlAttribute(name = "viewerState")
-        protected String viewerState;
-
-        /**
-         * Gets the value of the title property.
-         * 
-         * @return possible object is {@link String }
-         * 
-         */
-        public String getTitle()
-        {
-          return title;
-        }
-
-        /**
-         * Sets the value of the title property.
-         * 
-         * @param value
-         *          allowed object is {@link String }
-         * 
-         */
-        public void setTitle(String value)
-        {
-          this.title = value;
-        }
-
-        /**
-         * Gets the value of the annotationId property.
-         * 
-         * @return possible object is {@link String }
-         * 
-         */
-        public String getAnnotationId()
-        {
-          return annotationId;
-        }
-
-        /**
-         * Sets the value of the annotationId property.
-         * 
-         * @param value
-         *          allowed object is {@link String }
-         * 
-         */
-        public void setAnnotationId(String value)
-        {
-          this.annotationId = value;
-        }
-
-        /**
-         * Gets the value of the gapped property.
-         * 
-         * @return possible object is {@link Boolean }
-         * 
-         */
-        public Boolean isGapped()
-        {
-          return gapped;
-        }
-
-        /**
-         * Sets the value of the gapped property.
-         * 
-         * @param value
-         *          allowed object is {@link Boolean }
-         * 
-         */
-        public void setGapped(Boolean value)
-        {
-          this.gapped = value;
-        }
-
-        /**
-         * Gets the value of the viewerState property.
-         * 
-         * @return possible object is {@link String }
-         * 
-         */
-        public String getViewerState()
-        {
-          return viewerState;
-        }
-
-        /**
-         * Sets the value of the viewerState property.
-         * 
-         * @param value
-         *          allowed object is {@link String }
-         * 
-         */
-        public void setViewerState(String value)
-        {
-          this.viewerState = value;
-        }
-
-      }
-
-    }
-
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;sequence minOccurs="0">
-   *         &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
-   *         &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
-   *       &lt;/sequence>
-   *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-   *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-   *       &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "title", "newick" })
-  public static class Tree
-  {
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected String title;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected String newick;
-
-    @XmlAttribute(name = "fontName")
-    protected String fontName;
-
-    @XmlAttribute(name = "fontSize")
-    protected Integer fontSize;
-
-    @XmlAttribute(name = "fontStyle")
-    protected Integer fontStyle;
-
-    @XmlAttribute(name = "threshold")
-    protected Float threshold;
-
-    @XmlAttribute(name = "showBootstrap")
-    protected Boolean showBootstrap;
-
-    @XmlAttribute(name = "showDistances")
-    protected Boolean showDistances;
-
-    @XmlAttribute(name = "markUnlinked")
-    protected Boolean markUnlinked;
-
-    @XmlAttribute(name = "fitToWindow")
-    protected Boolean fitToWindow;
-
-    @XmlAttribute(name = "currentTree")
-    protected Boolean currentTree;
-
-    @XmlAttribute(name = "id")
-    @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
-    @XmlID
-    @XmlSchemaType(name = "ID")
-    protected String id;
-
-    @XmlAttribute(name = "width")
-    protected Integer width;
-
-    @XmlAttribute(name = "height")
-    protected Integer height;
-
-    @XmlAttribute(name = "xpos")
-    protected Integer xpos;
-
-    @XmlAttribute(name = "ypos")
-    protected Integer ypos;
-
-    /**
-     * Gets the value of the title property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getTitle()
-    {
-      return title;
-    }
-
-    /**
-     * Sets the value of the title property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setTitle(String value)
-    {
-      this.title = value;
-    }
-
-    /**
-     * Gets the value of the newick property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getNewick()
-    {
-      return newick;
-    }
-
-    /**
-     * Sets the value of the newick property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setNewick(String value)
-    {
-      this.newick = value;
-    }
-
-    /**
-     * Gets the value of the fontName property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getFontName()
-    {
-      return fontName;
-    }
-
-    /**
-     * Sets the value of the fontName property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setFontName(String value)
-    {
-      this.fontName = value;
-    }
-
-    /**
-     * Gets the value of the fontSize property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getFontSize()
-    {
-      return fontSize;
-    }
-
-    /**
-     * Sets the value of the fontSize property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setFontSize(Integer value)
-    {
-      this.fontSize = value;
-    }
-
-    /**
-     * Gets the value of the fontStyle property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getFontStyle()
-    {
-      return fontStyle;
-    }
-
-    /**
-     * Sets the value of the fontStyle property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setFontStyle(Integer value)
-    {
-      this.fontStyle = value;
-    }
-
-    /**
-     * Gets the value of the threshold property.
-     * 
-     * @return possible object is {@link Float }
-     * 
-     */
-    public Float getThreshold()
-    {
-      return threshold;
-    }
-
-    /**
-     * Sets the value of the threshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Float }
-     * 
-     */
-    public void setThreshold(Float value)
-    {
-      this.threshold = value;
-    }
-
-    /**
-     * Gets the value of the showBootstrap property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowBootstrap()
-    {
-      return showBootstrap;
-    }
-
-    /**
-     * Sets the value of the showBootstrap property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowBootstrap(Boolean value)
-    {
-      this.showBootstrap = value;
-    }
-
-    /**
-     * Gets the value of the showDistances property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowDistances()
-    {
-      return showDistances;
-    }
-
-    /**
-     * Sets the value of the showDistances property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowDistances(Boolean value)
-    {
-      this.showDistances = value;
-    }
-
-    /**
-     * Gets the value of the markUnlinked property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isMarkUnlinked()
-    {
-      return markUnlinked;
-    }
-
-    /**
-     * Sets the value of the markUnlinked property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setMarkUnlinked(Boolean value)
-    {
-      this.markUnlinked = value;
-    }
-
-    /**
-     * Gets the value of the fitToWindow property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isFitToWindow()
-    {
-      return fitToWindow;
-    }
-
-    /**
-     * Sets the value of the fitToWindow property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setFitToWindow(Boolean value)
-    {
-      this.fitToWindow = value;
-    }
-
-    /**
-     * Gets the value of the currentTree property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isCurrentTree()
-    {
-      return currentTree;
-    }
-
-    /**
-     * Sets the value of the currentTree property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setCurrentTree(Boolean value)
-    {
-      this.currentTree = value;
-    }
-
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getId()
-    {
-      return id;
-    }
-
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setId(String value)
-    {
-      this.id = value;
-    }
-
-    /**
-     * Gets the value of the width property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getWidth()
-    {
-      return width;
-    }
-
-    /**
-     * Sets the value of the width property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setWidth(Integer value)
-    {
-      this.width = value;
-    }
-
-    /**
-     * Gets the value of the height property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getHeight()
-    {
-      return height;
-    }
-
-    /**
-     * Sets the value of the height property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setHeight(Integer value)
-    {
-      this.height = value;
-    }
-
-    /**
-     * Gets the value of the xpos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getXpos()
-    {
-      return xpos;
-    }
-
-    /**
-     * Sets the value of the xpos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setXpos(Integer value)
-    {
-      this.xpos = value;
-    }
-
-    /**
-     * Gets the value of the ypos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getYpos()
-    {
-      return ypos;
-    }
-
-    /**
-     * Sets the value of the ypos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setYpos(Integer value)
-    {
-      this.ypos = value;
-    }
-
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;sequence>
-   *         &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
-   *       &lt;/sequence>
-   *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "userColourScheme" })
-  public static class UserColours
-  {
-
-    @XmlElement(
-      name = "UserColourScheme",
-      namespace = "www.jalview.org",
-      required = true)
-    protected JalviewUserColours userColourScheme;
-
-    @XmlAttribute(name = "id")
-    protected String id;
-
-    /**
-     * Gets the value of the userColourScheme property.
-     * 
-     * @return possible object is {@link JalviewUserColours }
-     * 
-     */
-    public JalviewUserColours getUserColourScheme()
-    {
-      return userColourScheme;
-    }
-
-    /**
-     * Sets the value of the userColourScheme property.
-     * 
-     * @param value
-     *          allowed object is {@link JalviewUserColours }
-     * 
-     */
-    public void setUserColourScheme(JalviewUserColours value)
-    {
-      this.userColourScheme = value;
-    }
-
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getId()
-    {
-      return id;
-    }
-
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setId(String value)
-    {
-      this.id = value;
-    }
-
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;sequence>
-   *         &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
-   *         &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
-   *           &lt;complexType>
-   *             &lt;complexContent>
-   *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *                 &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *               &lt;/restriction>
-   *             &lt;/complexContent>
-   *           &lt;/complexType>
-   *         &lt;/element>
-   *         &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
-   *           &lt;complexType>
-   *             &lt;complexContent>
-   *               &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
-   *                 &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *                 &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *               &lt;/extension>
-   *             &lt;/complexContent>
-   *           &lt;/complexType>
-   *         &lt;/element>
-   *       &lt;/sequence>
-   *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-   *       &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *       &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *       &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *       &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *       &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
-   *       &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(
-    name = "",
-    propOrder =
-    { "annotationColours", "hiddenColumns", "calcIdParam" })
-  public static class Viewport
-  {
-
-    @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
-    protected AnnotationColourScheme annotationColours;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List<JalviewModelType.Viewport.HiddenColumns> hiddenColumns;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List<JalviewModelType.Viewport.CalcIdParam> calcIdParam;
-
-    @XmlAttribute(name = "conservationSelected")
-    protected Boolean conservationSelected;
-
-    @XmlAttribute(name = "pidSelected")
-    protected Boolean pidSelected;
-
-    @XmlAttribute(name = "bgColour")
-    protected String bgColour;
-
-    @XmlAttribute(name = "consThreshold")
-    protected Integer consThreshold;
-
-    @XmlAttribute(name = "pidThreshold")
-    protected Integer pidThreshold;
-
-    @XmlAttribute(name = "title")
-    protected String title;
-
-    @XmlAttribute(name = "showFullId")
-    protected Boolean showFullId;
-
-    @XmlAttribute(name = "rightAlignIds")
-    protected Boolean rightAlignIds;
-
-    @XmlAttribute(name = "showText")
-    protected Boolean showText;
-
-    @XmlAttribute(name = "showColourText")
-    protected Boolean showColourText;
-
-    @XmlAttribute(name = "showUnconserved")
-    protected Boolean showUnconserved;
-
-    @XmlAttribute(name = "showBoxes")
-    protected Boolean showBoxes;
-
-    @XmlAttribute(name = "wrapAlignment")
-    protected Boolean wrapAlignment;
-
-    @XmlAttribute(name = "renderGaps")
-    protected Boolean renderGaps;
-
-    @XmlAttribute(name = "showSequenceFeatures")
-    protected Boolean showSequenceFeatures;
-
-    @XmlAttribute(name = "showNPfeatureTooltip")
-    protected Boolean showNPfeatureTooltip;
-
-    @XmlAttribute(name = "showDbRefTooltip")
-    protected Boolean showDbRefTooltip;
-
-    @XmlAttribute(name = "followHighlight")
-    protected Boolean followHighlight;
-
-    @XmlAttribute(name = "followSelection")
-    protected Boolean followSelection;
-
-    @XmlAttribute(name = "showAnnotation")
-    protected Boolean showAnnotation;
-
-    @XmlAttribute(name = "centreColumnLabels")
-    protected Boolean centreColumnLabels;
-
-    @XmlAttribute(name = "showGroupConservation")
-    protected Boolean showGroupConservation;
-
-    @XmlAttribute(name = "showGroupConsensus")
-    protected Boolean showGroupConsensus;
-
-    @XmlAttribute(name = "showConsensusHistogram")
-    protected Boolean showConsensusHistogram;
-
-    @XmlAttribute(name = "showSequenceLogo")
-    protected Boolean showSequenceLogo;
-
-    @XmlAttribute(name = "normaliseSequenceLogo")
-    protected Boolean normaliseSequenceLogo;
-
-    @XmlAttribute(name = "ignoreGapsinConsensus")
-    protected Boolean ignoreGapsinConsensus;
-
-    @XmlAttribute(name = "startRes")
-    protected Integer startRes;
-
-    @XmlAttribute(name = "startSeq")
-    protected Integer startSeq;
-
-    @XmlAttribute(name = "fontName")
-    protected String fontName;
-
-    @XmlAttribute(name = "fontSize")
-    protected Integer fontSize;
-
-    @XmlAttribute(name = "fontStyle")
-    protected Integer fontStyle;
-
-    @XmlAttribute(name = "scaleProteinAsCdna")
-    protected Boolean scaleProteinAsCdna;
-
-    @XmlAttribute(name = "viewName")
-    protected String viewName;
-
-    @XmlAttribute(name = "sequenceSetId")
-    protected String sequenceSetId;
-
-    @XmlAttribute(name = "gatheredViews")
-    protected Boolean gatheredViews;
-
-    @XmlAttribute(name = "textCol1")
-    protected Integer textCol1;
-
-    @XmlAttribute(name = "textCol2")
-    protected Integer textCol2;
-
-    @XmlAttribute(name = "textColThreshold")
-    protected Integer textColThreshold;
-
-    @XmlAttribute(name = "id")
-    @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
-    @XmlID
-    @XmlSchemaType(name = "ID")
-    protected String id;
-
-    @XmlAttribute(name = "complementId")
-    protected String complementId;
-
-    @XmlAttribute(name = "width")
-    protected Integer width;
-
-    @XmlAttribute(name = "height")
-    protected Integer height;
-
-    @XmlAttribute(name = "xpos")
-    protected Integer xpos;
-
-    @XmlAttribute(name = "ypos")
-    protected Integer ypos;
-
-    /**
-     * Gets the value of the annotationColours property.
-     * 
-     * @return possible object is {@link AnnotationColourScheme }
-     * 
-     */
-    public AnnotationColourScheme getAnnotationColours()
-    {
-      return annotationColours;
-    }
-
-    /**
-     * Sets the value of the annotationColours property.
-     * 
-     * @param value
-     *          allowed object is {@link AnnotationColourScheme }
-     * 
-     */
-    public void setAnnotationColours(AnnotationColourScheme value)
-    {
-      this.annotationColours = value;
-    }
-
-    /**
-     * Gets the value of the hiddenColumns property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the hiddenColumns property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * 
-     * <pre>
-     * getHiddenColumns().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModelType.Viewport.HiddenColumns }
-     * 
-     * 
-     */
-    public List<JalviewModelType.Viewport.HiddenColumns> getHiddenColumns()
-    {
-      if (hiddenColumns == null)
-      {
-        hiddenColumns = new ArrayList<JalviewModelType.Viewport.HiddenColumns>();
-      }
-      return this.hiddenColumns;
-    }
-
-    /**
-     * Gets the value of the calcIdParam property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the calcIdParam property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * 
-     * <pre>
-     * getCalcIdParam().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModelType.Viewport.CalcIdParam }
-     * 
-     * 
-     */
-    public List<JalviewModelType.Viewport.CalcIdParam> getCalcIdParam()
-    {
-      if (calcIdParam == null)
-      {
-        calcIdParam = new ArrayList<JalviewModelType.Viewport.CalcIdParam>();
-      }
-      return this.calcIdParam;
-    }
-
-    /**
-     * Gets the value of the conservationSelected property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isConservationSelected()
-    {
-      return conservationSelected;
-    }
-
-    /**
-     * Sets the value of the conservationSelected property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setConservationSelected(Boolean value)
-    {
-      this.conservationSelected = value;
-    }
-
-    /**
-     * Gets the value of the pidSelected property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isPidSelected()
-    {
-      return pidSelected;
-    }
-
-    /**
-     * Sets the value of the pidSelected property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setPidSelected(Boolean value)
-    {
-      this.pidSelected = value;
-    }
-
-    /**
-     * Gets the value of the bgColour property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getBgColour()
-    {
-      return bgColour;
-    }
-
-    /**
-     * Sets the value of the bgColour property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setBgColour(String value)
-    {
-      this.bgColour = value;
-    }
-
-    /**
-     * Gets the value of the consThreshold property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getConsThreshold()
-    {
-      return consThreshold;
-    }
-
-    /**
-     * Sets the value of the consThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setConsThreshold(Integer value)
-    {
-      this.consThreshold = value;
-    }
-
-    /**
-     * Gets the value of the pidThreshold property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getPidThreshold()
-    {
-      return pidThreshold;
-    }
-
-    /**
-     * Sets the value of the pidThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setPidThreshold(Integer value)
-    {
-      this.pidThreshold = value;
-    }
-
-    /**
-     * Gets the value of the title property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getTitle()
-    {
-      return title;
-    }
-
-    /**
-     * Sets the value of the title property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setTitle(String value)
-    {
-      this.title = value;
-    }
-
-    /**
-     * Gets the value of the showFullId property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowFullId()
-    {
-      return showFullId;
-    }
-
-    /**
-     * Sets the value of the showFullId property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowFullId(Boolean value)
-    {
-      this.showFullId = value;
-    }
-
-    /**
-     * Gets the value of the rightAlignIds property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isRightAlignIds()
-    {
-      return rightAlignIds;
-    }
-
-    /**
-     * Sets the value of the rightAlignIds property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setRightAlignIds(Boolean value)
-    {
-      this.rightAlignIds = value;
-    }
-
-    /**
-     * Gets the value of the showText property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowText()
-    {
-      return showText;
-    }
-
-    /**
-     * Sets the value of the showText property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowText(Boolean value)
-    {
-      this.showText = value;
-    }
-
-    /**
-     * Gets the value of the showColourText property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowColourText()
-    {
-      return showColourText;
-    }
-
-    /**
-     * Sets the value of the showColourText property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowColourText(Boolean value)
-    {
-      this.showColourText = value;
-    }
-
-    /**
-     * Gets the value of the showUnconserved property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowUnconserved()
-    {
-      if (showUnconserved == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showUnconserved;
-      }
-    }
-
-    /**
-     * Sets the value of the showUnconserved property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowUnconserved(Boolean value)
-    {
-      this.showUnconserved = value;
-    }
-
-    /**
-     * Gets the value of the showBoxes property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowBoxes()
-    {
-      return showBoxes;
-    }
-
-    /**
-     * Sets the value of the showBoxes property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowBoxes(Boolean value)
-    {
-      this.showBoxes = value;
-    }
-
-    /**
-     * Gets the value of the wrapAlignment property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isWrapAlignment()
-    {
-      return wrapAlignment;
-    }
-
-    /**
-     * Sets the value of the wrapAlignment property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setWrapAlignment(Boolean value)
-    {
-      this.wrapAlignment = value;
-    }
-
-    /**
-     * Gets the value of the renderGaps property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isRenderGaps()
-    {
-      return renderGaps;
-    }
-
-    /**
-     * Sets the value of the renderGaps property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setRenderGaps(Boolean value)
-    {
-      this.renderGaps = value;
-    }
-
-    /**
-     * Gets the value of the showSequenceFeatures property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowSequenceFeatures()
-    {
-      return showSequenceFeatures;
-    }
-
-    /**
-     * Sets the value of the showSequenceFeatures property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowSequenceFeatures(Boolean value)
-    {
-      this.showSequenceFeatures = value;
-    }
-
-    /**
-     * Gets the value of the showNPfeatureTooltip property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowNPfeatureTooltip()
-    {
-      return showNPfeatureTooltip;
-    }
-
-    /**
-     * Sets the value of the showNPfeatureTooltip property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowNPfeatureTooltip(Boolean value)
-    {
-      this.showNPfeatureTooltip = value;
-    }
-
-    /**
-     * Gets the value of the showDbRefTooltip property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowDbRefTooltip()
-    {
-      return showDbRefTooltip;
-    }
-
-    /**
-     * Sets the value of the showDbRefTooltip property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowDbRefTooltip(Boolean value)
-    {
-      this.showDbRefTooltip = value;
-    }
-
-    /**
-     * Gets the value of the followHighlight property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isFollowHighlight()
-    {
-      if (followHighlight == null)
-      {
-        return true;
-      }
-      else
-      {
-        return followHighlight;
-      }
-    }
-
-    /**
-     * Sets the value of the followHighlight property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setFollowHighlight(Boolean value)
-    {
-      this.followHighlight = value;
-    }
-
-    /**
-     * Gets the value of the followSelection property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isFollowSelection()
-    {
-      if (followSelection == null)
-      {
-        return true;
-      }
-      else
-      {
-        return followSelection;
-      }
-    }
-
-    /**
-     * Sets the value of the followSelection property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setFollowSelection(Boolean value)
-    {
-      this.followSelection = value;
-    }
-
-    /**
-     * Gets the value of the showAnnotation property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowAnnotation()
-    {
-      return showAnnotation;
-    }
-
-    /**
-     * Sets the value of the showAnnotation property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowAnnotation(Boolean value)
-    {
-      this.showAnnotation = value;
-    }
-
-    /**
-     * Gets the value of the centreColumnLabels property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isCentreColumnLabels()
-    {
-      if (centreColumnLabels == null)
-      {
-        return false;
-      }
-      else
-      {
-        return centreColumnLabels;
-      }
-    }
-
-    /**
-     * Sets the value of the centreColumnLabels property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setCentreColumnLabels(Boolean value)
-    {
-      this.centreColumnLabels = value;
-    }
-
-    /**
-     * Gets the value of the showGroupConservation property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowGroupConservation()
-    {
-      if (showGroupConservation == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showGroupConservation;
-      }
-    }
-
-    /**
-     * Sets the value of the showGroupConservation property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowGroupConservation(Boolean value)
-    {
-      this.showGroupConservation = value;
-    }
-
-    /**
-     * Gets the value of the showGroupConsensus property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowGroupConsensus()
-    {
-      if (showGroupConsensus == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showGroupConsensus;
-      }
-    }
-
-    /**
-     * Sets the value of the showGroupConsensus property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowGroupConsensus(Boolean value)
-    {
-      this.showGroupConsensus = value;
-    }
-
-    /**
-     * Gets the value of the showConsensusHistogram property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowConsensusHistogram()
-    {
-      if (showConsensusHistogram == null)
-      {
-        return true;
-      }
-      else
-      {
-        return showConsensusHistogram;
-      }
-    }
-
-    /**
-     * Sets the value of the showConsensusHistogram property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowConsensusHistogram(Boolean value)
-    {
-      this.showConsensusHistogram = value;
-    }
-
-    /**
-     * Gets the value of the showSequenceLogo property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowSequenceLogo()
-    {
-      if (showSequenceLogo == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showSequenceLogo;
-      }
-    }
-
-    /**
-     * Sets the value of the showSequenceLogo property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowSequenceLogo(Boolean value)
-    {
-      this.showSequenceLogo = value;
-    }
-
-    /**
-     * Gets the value of the normaliseSequenceLogo property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isNormaliseSequenceLogo()
-    {
-      if (normaliseSequenceLogo == null)
-      {
-        return false;
-      }
-      else
-      {
-        return normaliseSequenceLogo;
-      }
-    }
-
-    /**
-     * Sets the value of the normaliseSequenceLogo property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setNormaliseSequenceLogo(Boolean value)
-    {
-      this.normaliseSequenceLogo = value;
-    }
-
-    /**
-     * Gets the value of the ignoreGapsinConsensus property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isIgnoreGapsinConsensus()
-    {
-      if (ignoreGapsinConsensus == null)
-      {
-        return true;
-      }
-      else
-      {
-        return ignoreGapsinConsensus;
-      }
-    }
-
-    /**
-     * Sets the value of the ignoreGapsinConsensus property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setIgnoreGapsinConsensus(Boolean value)
-    {
-      this.ignoreGapsinConsensus = value;
-    }
-
-    /**
-     * Gets the value of the startRes property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getStartRes()
-    {
-      return startRes;
-    }
-
-    /**
-     * Sets the value of the startRes property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setStartRes(Integer value)
-    {
-      this.startRes = value;
-    }
-
-    /**
-     * Gets the value of the startSeq property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getStartSeq()
-    {
-      return startSeq;
-    }
-
-    /**
-     * Sets the value of the startSeq property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setStartSeq(Integer value)
-    {
-      this.startSeq = value;
-    }
-
-    /**
-     * Gets the value of the fontName property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getFontName()
-    {
-      return fontName;
-    }
-
-    /**
-     * Sets the value of the fontName property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setFontName(String value)
-    {
-      this.fontName = value;
-    }
-
-    /**
-     * Gets the value of the fontSize property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getFontSize()
-    {
-      return fontSize;
-    }
-
-    /**
-     * Sets the value of the fontSize property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setFontSize(Integer value)
-    {
-      this.fontSize = value;
-    }
-
-    /**
-     * Gets the value of the fontStyle property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getFontStyle()
-    {
-      return fontStyle;
-    }
-
-    /**
-     * Sets the value of the fontStyle property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setFontStyle(Integer value)
-    {
-      this.fontStyle = value;
-    }
-
-    /**
-     * Gets the value of the scaleProteinAsCdna property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isScaleProteinAsCdna()
-    {
-      if (scaleProteinAsCdna == null)
-      {
-        return true;
-      }
-      else
-      {
-        return scaleProteinAsCdna;
-      }
-    }
-
-    /**
-     * Sets the value of the scaleProteinAsCdna property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setScaleProteinAsCdna(Boolean value)
-    {
-      this.scaleProteinAsCdna = value;
-    }
-
-    /**
-     * Gets the value of the viewName property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getViewName()
-    {
-      return viewName;
-    }
-
-    /**
-     * Sets the value of the viewName property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setViewName(String value)
-    {
-      this.viewName = value;
-    }
-
-    /**
-     * Gets the value of the sequenceSetId property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getSequenceSetId()
-    {
-      return sequenceSetId;
-    }
-
-    /**
-     * Sets the value of the sequenceSetId property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setSequenceSetId(String value)
-    {
-      this.sequenceSetId = value;
-    }
-
-    /**
-     * Gets the value of the gatheredViews property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isGatheredViews()
-    {
-      return gatheredViews;
-    }
-
-    /**
-     * Sets the value of the gatheredViews property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setGatheredViews(Boolean value)
-    {
-      this.gatheredViews = value;
-    }
-
-    /**
-     * Gets the value of the textCol1 property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getTextCol1()
-    {
-      return textCol1;
-    }
-
-    /**
-     * Sets the value of the textCol1 property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextCol1(Integer value)
-    {
-      this.textCol1 = value;
-    }
-
-    /**
-     * Gets the value of the textCol2 property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getTextCol2()
-    {
-      return textCol2;
-    }
-
-    /**
-     * Sets the value of the textCol2 property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextCol2(Integer value)
-    {
-      this.textCol2 = value;
-    }
-
-    /**
-     * Gets the value of the textColThreshold property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getTextColThreshold()
-    {
-      return textColThreshold;
-    }
-
-    /**
-     * Sets the value of the textColThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextColThreshold(Integer value)
-    {
-      this.textColThreshold = value;
-    }
-
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getId()
-    {
-      return id;
-    }
-
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setId(String value)
-    {
-      this.id = value;
-    }
-
-    /**
-     * Gets the value of the complementId property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getComplementId()
-    {
-      return complementId;
-    }
-
-    /**
-     * Sets the value of the complementId property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setComplementId(String value)
-    {
-      this.complementId = value;
-    }
-
-    /**
-     * Gets the value of the width property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getWidth()
-    {
-      return width;
-    }
-
-    /**
-     * Sets the value of the width property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setWidth(Integer value)
-    {
-      this.width = value;
-    }
-
-    /**
-     * Gets the value of the height property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getHeight()
-    {
-      return height;
-    }
-
-    /**
-     * Sets the value of the height property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setHeight(Integer value)
-    {
-      this.height = value;
-    }
-
-    /**
-     * Gets the value of the xpos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getXpos()
-    {
-      return xpos;
-    }
-
-    /**
-     * Sets the value of the xpos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setXpos(Integer value)
-    {
-      this.xpos = value;
-    }
-
-    /**
-     * Gets the value of the ypos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getYpos()
-    {
-      return ypos;
-    }
-
-    /**
-     * Sets the value of the ypos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setYpos(Integer value)
-    {
-      this.ypos = value;
-    }
-
-    /**
-     * <p>
-     * Java class for anonymous complex type.
-     * 
-     * <p>
-     * The following schema fragment specifies the expected content contained
-     * within this class.
-     * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
-     *       &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     &lt;/extension>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class CalcIdParam extends WebServiceParameterSet
-    {
-
-      @XmlAttribute(name = "calcId", required = true)
-      protected String calcId;
-
-      @XmlAttribute(name = "needsUpdate")
-      protected Boolean needsUpdate;
-
-      @XmlAttribute(name = "autoUpdate", required = true)
-      protected boolean autoUpdate;
-
-      /**
-       * Gets the value of the calcId property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getCalcId()
-      {
-        return calcId;
-      }
-
-      /**
-       * Sets the value of the calcId property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setCalcId(String value)
-      {
-        this.calcId = value;
-      }
-
-      /**
-       * Gets the value of the needsUpdate property.
-       * 
-       * @return possible object is {@link Boolean }
-       * 
-       */
-      public boolean isNeedsUpdate()
-      {
-        if (needsUpdate == null)
-        {
-          return false;
-        }
-        else
-        {
-          return needsUpdate;
-        }
-      }
-
-      /**
-       * Sets the value of the needsUpdate property.
-       * 
-       * @param value
-       *          allowed object is {@link Boolean }
-       * 
-       */
-      public void setNeedsUpdate(Boolean value)
-      {
-        this.needsUpdate = value;
-      }
-
-      /**
-       * Gets the value of the autoUpdate property.
-       * 
-       */
-      public boolean isAutoUpdate()
-      {
-        return autoUpdate;
-      }
-
-      /**
-       * Sets the value of the autoUpdate property.
-       * 
-       */
-      public void setAutoUpdate(boolean value)
-      {
-        this.autoUpdate = value;
-      }
-
-    }
-
-    /**
-     * <p>
-     * Java class for anonymous complex type.
-     * 
-     * <p>
-     * The following schema fragment specifies the expected content contained
-     * within this class.
-     * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class HiddenColumns
-    {
-
-      @XmlAttribute(name = "start")
-      protected Integer start;
-
-      @XmlAttribute(name = "end")
-      protected Integer end;
-
-      /**
-       * Gets the value of the start property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getStart()
-      {
-        return start;
-      }
-
-      /**
-       * Sets the value of the start property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setStart(Integer value)
-      {
-        this.start = value;
-      }
-
-      /**
-       * Gets the value of the end property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getEnd()
-      {
-        return end;
-      }
-
-      /**
-       * Sets the value of the end property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setEnd(Integer value)
-      {
-        this.end = value;
-      }
-
-    }
-
-  }
-
-}
diff --git a/src/jalview/xml/binding/jalview/JalviewUserColours.java b/src/jalview/xml/binding/jalview/JalviewUserColours.java
index be68266..21abacb 100644
--- a/src/jalview/xml/binding/jalview/JalviewUserColours.java
+++ b/src/jalview/xml/binding/jalview/JalviewUserColours.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -15,585 +16,597 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * &lt;p&gt;Java class for JalviewUserColours complex type.
+ * <p>Java class for JalviewUserColours complex type.
  * 
- * &lt;p&gt;The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
- * &lt;pre&gt; &amp;lt;complexType name="JalviewUserColours"&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="Version"
- * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&amp;gt;
- * &amp;lt;element name="colour" maxOccurs="unbounded" minOccurs="0"&amp;gt;
- * &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
- * &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="attributeName"
- * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
- * minOccurs="0"/&amp;gt; &amp;lt;/sequence&amp;gt; &amp;lt;attribute
- * name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;attribute name="RGB" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
- * name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;attribute name="noValueColour"
- * type="{www.jalview.org/colours}NoValueColour" default="Min" /&amp;gt;
- * &amp;lt;attribute name="threshType"
- * type="{www.jalview.org/colours}ThresholdType" /&amp;gt; &amp;lt;attribute
- * name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
- * &amp;lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
- * /&amp;gt; &amp;lt;attribute name="min"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt; &amp;lt;attribute
- * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&amp;gt; &amp;lt;attribute name="autoScale"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
- * name="filter" maxOccurs="unbounded" minOccurs="0"&amp;gt;
- * &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
- * &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="matcherSet"
- * type="{www.jalview.org/colours}FeatureMatcherSet"/&amp;gt;
- * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="featureType" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
- * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="schemeName"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
+ * <pre>
+ * &lt;complexType name="JalviewUserColours">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         &lt;element name="colour" maxOccurs="unbounded" minOccurs="0">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;sequence>
+ *                   &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ *                 &lt;/sequence>
+ *                 &lt;attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ *                 &lt;attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
+ *                 &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                 &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                 &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                 &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                 &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *         &lt;element name="filter" maxOccurs="unbounded" minOccurs="0">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;sequence>
+ *                   &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
+ *                 &lt;/sequence>
+ *                 &lt;attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *       &lt;/sequence>
+ *       &lt;attribute name="schemeName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "JalviewUserColours",
-  namespace = "www.jalview.org/colours",
-  propOrder =
-  { "version", "colour", "filter" })
-public class JalviewUserColours
-{
-
-  @XmlElement(name = "Version", namespace = "")
-  protected String version;
-
-  @XmlElement(namespace = "")
-  protected List<JalviewUserColours.Colour> colour;
-
-  @XmlElement(namespace = "")
-  protected List<JalviewUserColours.Filter> filter;
-
-  @XmlAttribute(name = "schemeName")
-  protected String schemeName;
-
-  /**
-   * Gets the value of the version property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getVersion()
-  {
-    return version;
-  }
-
-  /**
-   * Sets the value of the version property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setVersion(String value)
-  {
-    this.version = value;
-  }
-
-  /**
-   * Gets the value of the colour property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the colour property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getColour().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link JalviewUserColours.Colour }
-   * 
-   * 
-   */
-  public List<JalviewUserColours.Colour> getColour()
-  {
-    if (colour == null)
-    {
-      colour = new ArrayList<JalviewUserColours.Colour>();
-    }
-    return this.colour;
-  }
-
-  /**
-   * Gets the value of the filter property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the filter property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getFilter().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link JalviewUserColours.Filter }
-   * 
-   * 
-   */
-  public List<JalviewUserColours.Filter> getFilter()
-  {
-    if (filter == null)
-    {
-      filter = new ArrayList<JalviewUserColours.Filter>();
-    }
-    return this.filter;
-  }
-
-  /**
-   * Gets the value of the schemeName property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getSchemeName()
-  {
-    return schemeName;
-  }
-
-  /**
-   * Sets the value of the schemeName property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setSchemeName(String value)
-  {
-    this.schemeName = value;
-  }
-
-  /**
-   * &lt;p&gt;Java class for anonymous complex type.
-   * 
-   * &lt;p&gt;The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-   * &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
-   * &amp;lt;sequence&amp;gt; &amp;lt;element name="attributeName"
-   * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
-   * minOccurs="0"/&amp;gt; &amp;lt;/sequence&amp;gt; &amp;lt;attribute
-   * name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-   * &amp;lt;attribute name="RGB" use="required"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
-   * name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-   * &amp;lt;attribute name="noValueColour"
-   * type="{www.jalview.org/colours}NoValueColour" default="Min" /&amp;gt;
-   * &amp;lt;attribute name="threshType"
-   * type="{www.jalview.org/colours}ThresholdType" /&amp;gt; &amp;lt;attribute
-   * name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
-   * &amp;lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
-   * /&amp;gt; &amp;lt;attribute name="min"
-   * type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt; &amp;lt;attribute
-   * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
-   * /&amp;gt; &amp;lt;attribute name="autoScale"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
-   * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "attributeName" })
-  public static class Colour
-  {
-
+@XmlType(name = "JalviewUserColours", namespace = "www.jalview.org/colours", propOrder = {
+    "version",
+    "colour",
+    "filter"
+})
+public class JalviewUserColours {
+
+    @XmlElement(name = "Version", namespace = "")
+    protected String version;
     @XmlElement(namespace = "")
-    protected List<String> attributeName;
-
-    @XmlAttribute(name = "Name")
-    protected String name;
-
-    @XmlAttribute(name = "RGB", required = true)
-    protected String rgb;
-
-    @XmlAttribute(name = "minRGB")
-    protected String minRGB;
-
-    @XmlAttribute(name = "noValueColour")
-    protected NoValueColour noValueColour;
-
-    @XmlAttribute(name = "threshType")
-    protected ThresholdType threshType;
-
-    @XmlAttribute(name = "threshold")
-    protected Float threshold;
-
-    @XmlAttribute(name = "max")
-    protected Float max;
-
-    @XmlAttribute(name = "min")
-    protected Float min;
-
-    @XmlAttribute(name = "colourByLabel")
-    protected Boolean colourByLabel;
-
-    @XmlAttribute(name = "autoScale")
-    protected Boolean autoScale;
-
-    /**
-     * Gets the value of the attributeName property.
-     * 
-     * &lt;p&gt; This accessor method returns a reference to the live list, not
-     * a snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * &lt;CODE&gt;set&lt;/CODE&gt; method for the attributeName property.
-     * 
-     * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-     * getAttributeName().add(newItem); &lt;/pre&gt;
-     * 
-     * 
-     * &lt;p&gt; Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
-     * 
-     */
-    public List<String> getAttributeName()
-    {
-      if (attributeName == null)
-      {
-        attributeName = new ArrayList<String>();
-      }
-      return this.attributeName;
-    }
-
-    /**
-     * Gets the value of the name property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getName()
-    {
-      return name;
-    }
-
-    /**
-     * Sets the value of the name property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setName(String value)
-    {
-      this.name = value;
-    }
-
-    /**
-     * Gets the value of the rgb property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getRGB()
-    {
-      return rgb;
-    }
-
-    /**
-     * Sets the value of the rgb property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setRGB(String value)
-    {
-      this.rgb = value;
-    }
-
-    /**
-     * Gets the value of the minRGB property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getMinRGB()
-    {
-      return minRGB;
-    }
-
-    /**
-     * Sets the value of the minRGB property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setMinRGB(String value)
-    {
-      this.minRGB = value;
-    }
+    protected List<JalviewUserColours.Colour> colour;
+    @XmlElement(namespace = "")
+    protected List<JalviewUserColours.Filter> filter;
+    @XmlAttribute(name = "schemeName")
+    protected String schemeName;
 
     /**
-     * Gets the value of the noValueColour property.
-     * 
-     * @return possible object is {@link NoValueColour }
+     * Gets the value of the version property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public NoValueColour getNoValueColour()
-    {
-      if (noValueColour == null)
-      {
-        return NoValueColour.MIN;
-      }
-      else
-      {
-        return noValueColour;
-      }
+    public String getVersion() {
+        return version;
     }
 
     /**
-     * Sets the value of the noValueColour property.
+     * Sets the value of the version property.
      * 
      * @param value
-     *          allowed object is {@link NoValueColour }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setNoValueColour(NoValueColour value)
-    {
-      this.noValueColour = value;
+    public void setVersion(String value) {
+        this.version = value;
     }
 
     /**
-     * Gets the value of the threshType property.
+     * Gets the value of the colour property.
      * 
-     * @return possible object is {@link ThresholdType }
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the colour property.
      * 
-     */
-    public ThresholdType getThreshType()
-    {
-      return threshType;
-    }
-
-    /**
-     * Sets the value of the threshType property.
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getColour().add(newItem);
+     * </pre>
      * 
-     * @param value
-     *          allowed object is {@link ThresholdType }
      * 
-     */
-    public void setThreshType(ThresholdType value)
-    {
-      this.threshType = value;
-    }
-
-    /**
-     * Gets the value of the threshold property.
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewUserColours.Colour }
      * 
-     * @return possible object is {@link Float }
      * 
      */
-    public Float getThreshold()
-    {
-      return threshold;
+    public List<JalviewUserColours.Colour> getColour() {
+        if (colour == null) {
+            colour = new ArrayList<JalviewUserColours.Colour>();
+        }
+        return this.colour;
     }
 
     /**
-     * Sets the value of the threshold property.
+     * Gets the value of the filter property.
      * 
-     * @param value
-     *          allowed object is {@link Float }
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the filter property.
      * 
-     */
-    public void setThreshold(Float value)
-    {
-      this.threshold = value;
-    }
-
-    /**
-     * Gets the value of the max property.
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getFilter().add(newItem);
+     * </pre>
      * 
-     * @return possible object is {@link Float }
      * 
-     */
-    public Float getMax()
-    {
-      return max;
-    }
-
-    /**
-     * Sets the value of the max property.
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewUserColours.Filter }
      * 
-     * @param value
-     *          allowed object is {@link Float }
      * 
      */
-    public void setMax(Float value)
-    {
-      this.max = value;
+    public List<JalviewUserColours.Filter> getFilter() {
+        if (filter == null) {
+            filter = new ArrayList<JalviewUserColours.Filter>();
+        }
+        return this.filter;
     }
 
     /**
-     * Gets the value of the min property.
-     * 
-     * @return possible object is {@link Float }
+     * Gets the value of the schemeName property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public Float getMin()
-    {
-      return min;
+    public String getSchemeName() {
+        return schemeName;
     }
 
     /**
-     * Sets the value of the min property.
+     * Sets the value of the schemeName property.
      * 
      * @param value
-     *          allowed object is {@link Float }
-     * 
-     */
-    public void setMin(Float value)
-    {
-      this.min = value;
-    }
-
-    /**
-     * Gets the value of the colourByLabel property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public Boolean isColourByLabel()
-    {
-      return colourByLabel;
+    public void setSchemeName(String value) {
+        this.schemeName = value;
     }
 
-    /**
-     * Sets the value of the colourByLabel property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setColourByLabel(Boolean value)
-    {
-      this.colourByLabel = value;
-    }
 
     /**
-     * Gets the value of the autoScale property.
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+     *       &lt;/sequence>
+     *       &lt;attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+     *       &lt;attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
+     *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
      * 
-     * @return possible object is {@link Boolean }
      * 
      */
-    public Boolean isAutoScale()
-    {
-      return autoScale;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "attributeName"
+    })
+    public static class Colour {
+
+        @XmlElement(namespace = "")
+        protected List<String> attributeName;
+        @XmlAttribute(name = "Name")
+        protected String name;
+        @XmlAttribute(name = "RGB", required = true)
+        protected String rgb;
+        @XmlAttribute(name = "minRGB")
+        protected String minRGB;
+        @XmlAttribute(name = "noValueColour")
+        protected NoValueColour noValueColour;
+        @XmlAttribute(name = "threshType")
+        protected ThresholdType threshType;
+        @XmlAttribute(name = "threshold")
+        protected Float threshold;
+        @XmlAttribute(name = "max")
+        protected Float max;
+        @XmlAttribute(name = "min")
+        protected Float min;
+        @XmlAttribute(name = "colourByLabel")
+        protected Boolean colourByLabel;
+        @XmlAttribute(name = "autoScale")
+        protected Boolean autoScale;
+
+        /**
+         * Gets the value of the attributeName property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the attributeName property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getAttributeName().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link String }
+         * 
+         * 
+         */
+        public List<String> getAttributeName() {
+            if (attributeName == null) {
+                attributeName = new ArrayList<String>();
+            }
+            return this.attributeName;
+        }
+
+        /**
+         * Gets the value of the name property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getName() {
+            return name;
+        }
+
+        /**
+         * Sets the value of the name property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setName(String value) {
+            this.name = value;
+        }
+
+        /**
+         * Gets the value of the rgb property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getRGB() {
+            return rgb;
+        }
+
+        /**
+         * Sets the value of the rgb property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setRGB(String value) {
+            this.rgb = value;
+        }
+
+        /**
+         * Gets the value of the minRGB property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getMinRGB() {
+            return minRGB;
+        }
+
+        /**
+         * Sets the value of the minRGB property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setMinRGB(String value) {
+            this.minRGB = value;
+        }
+
+        /**
+         * Gets the value of the noValueColour property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link NoValueColour }
+         *     
+         */
+        public NoValueColour getNoValueColour() {
+            if (noValueColour == null) {
+                return NoValueColour.MIN;
+            } else {
+                return noValueColour;
+            }
+        }
+
+        /**
+         * Sets the value of the noValueColour property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link NoValueColour }
+         *     
+         */
+        public void setNoValueColour(NoValueColour value) {
+            this.noValueColour = value;
+        }
+
+        /**
+         * Gets the value of the threshType property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link ThresholdType }
+         *     
+         */
+        public ThresholdType getThreshType() {
+            return threshType;
+        }
+
+        /**
+         * Sets the value of the threshType property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link ThresholdType }
+         *     
+         */
+        public void setThreshType(ThresholdType value) {
+            this.threshType = value;
+        }
+
+        /**
+         * Gets the value of the threshold property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Float }
+         *     
+         */
+        public Float getThreshold() {
+            return threshold;
+        }
+
+        /**
+         * Sets the value of the threshold property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Float }
+         *     
+         */
+        public void setThreshold(Float value) {
+            this.threshold = value;
+        }
+
+        /**
+         * Gets the value of the max property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Float }
+         *     
+         */
+        public Float getMax() {
+            return max;
+        }
+
+        /**
+         * Sets the value of the max property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Float }
+         *     
+         */
+        public void setMax(Float value) {
+            this.max = value;
+        }
+
+        /**
+         * Gets the value of the min property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Float }
+         *     
+         */
+        public Float getMin() {
+            return min;
+        }
+
+        /**
+         * Sets the value of the min property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Float }
+         *     
+         */
+        public void setMin(Float value) {
+            this.min = value;
+        }
+
+        /**
+         * Gets the value of the colourByLabel property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isColourByLabel() {
+            return colourByLabel;
+        }
+
+        /**
+         * Sets the value of the colourByLabel property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setColourByLabel(Boolean value) {
+            this.colourByLabel = value;
+        }
+
+        /**
+         * Gets the value of the autoScale property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isAutoScale() {
+            return autoScale;
+        }
+
+        /**
+         * Sets the value of the autoScale property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setAutoScale(Boolean value) {
+            this.autoScale = value;
+        }
 
-    /**
-     * Sets the value of the autoScale property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setAutoScale(Boolean value)
-    {
-      this.autoScale = value;
     }
 
-  }
-
-  /**
-   * &lt;p&gt;Java class for anonymous complex type.
-   * 
-   * &lt;p&gt;The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-   * &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
-   * &amp;lt;sequence&amp;gt; &amp;lt;element name="matcherSet"
-   * type="{www.jalview.org/colours}FeatureMatcherSet"/&amp;gt;
-   * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="featureType"
-   * use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-   * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "matcherSet" })
-  public static class Filter
-  {
-
-    @XmlElement(namespace = "", required = true)
-    protected FeatureMatcherSet matcherSet;
-
-    @XmlAttribute(name = "featureType", required = true)
-    protected String featureType;
 
     /**
-     * Gets the value of the matcherSet property.
+     * <p>Java class for anonymous complex type.
      * 
-     * @return possible object is {@link FeatureMatcherSet }
+     * <p>The following schema fragment specifies the expected content contained within this class.
      * 
-     */
-    public FeatureMatcherSet getMatcherSet()
-    {
-      return matcherSet;
-    }
-
-    /**
-     * Sets the value of the matcherSet property.
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
+     *       &lt;/sequence>
+     *       &lt;attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
      * 
-     * @param value
-     *          allowed object is {@link FeatureMatcherSet }
      * 
      */
-    public void setMatcherSet(FeatureMatcherSet value)
-    {
-      this.matcherSet = value;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "matcherSet"
+    })
+    public static class Filter {
+
+        @XmlElement(namespace = "", required = true)
+        protected FeatureMatcherSet matcherSet;
+        @XmlAttribute(name = "featureType", required = true)
+        protected String featureType;
+
+        /**
+         * Gets the value of the matcherSet property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link FeatureMatcherSet }
+         *     
+         */
+        public FeatureMatcherSet getMatcherSet() {
+            return matcherSet;
+        }
+
+        /**
+         * Sets the value of the matcherSet property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link FeatureMatcherSet }
+         *     
+         */
+        public void setMatcherSet(FeatureMatcherSet value) {
+            this.matcherSet = value;
+        }
+
+        /**
+         * Gets the value of the featureType property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getFeatureType() {
+            return featureType;
+        }
+
+        /**
+         * Sets the value of the featureType property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setFeatureType(String value) {
+            this.featureType = value;
+        }
 
-    /**
-     * Gets the value of the featureType property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getFeatureType()
-    {
-      return featureType;
     }
 
-    /**
-     * Sets the value of the featureType property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setFeatureType(String value)
-    {
-      this.featureType = value;
-    }
-
-  }
-
 }
diff --git a/src/jalview/xml/binding/jalview/MapListType.java b/src/jalview/xml/binding/jalview/MapListType.java
index edc69b4..99c5b4b 100644
--- a/src/jalview/xml/binding/jalview/MapListType.java
+++ b/src/jalview/xml/binding/jalview/MapListType.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.math.BigInteger;
@@ -17,291 +18,298 @@ import javax.xml.bind.annotation.XmlSchemaType;
 import javax.xml.bind.annotation.XmlSeeAlso;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
  * 
- * This effectively represents a java.util.MapList object
+ * 				This effectively represents a java.util.MapList object
+ * 			
  * 
+ * <p>Java class for mapListType complex type.
  * 
- * &lt;p&gt;Java class for mapListType complex type.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
- * &lt;p&gt;The following schema fragment specifies the expected content
- * contained within this class.
- * 
- * &lt;pre&gt; &amp;lt;complexType name="mapListType"&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="mapListFrom"
- * maxOccurs="unbounded" minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
- * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&amp;gt; &amp;lt;attribute name="end" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
- * name="mapListTo" maxOccurs="unbounded" minOccurs="0"&amp;gt;
- * &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
- * &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;attribute name="start" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
- * name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&amp;gt; &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
- * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="mapFromUnit" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}positiveInteger" /&amp;gt;
- * &amp;lt;attribute name="mapToUnit" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}positiveInteger" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
+ * <pre>
+ * &lt;complexType name="mapListType">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="mapListFrom" maxOccurs="unbounded" minOccurs="0">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                 &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *         &lt;element name="mapListTo" maxOccurs="unbounded" minOccurs="0">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                 &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *       &lt;/sequence>
+ *       &lt;attribute name="mapFromUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" />
+ *       &lt;attribute name="mapToUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" />
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "mapListType", propOrder = { "mapListFrom", "mapListTo" })
-@XmlSeeAlso({ Mapping.class })
-public class MapListType
-{
-
-  protected List<MapListType.MapListFrom> mapListFrom;
-
-  protected List<MapListType.MapListTo> mapListTo;
-
-  @XmlAttribute(name = "mapFromUnit", required = true)
-  @XmlSchemaType(name = "positiveInteger")
-  protected BigInteger mapFromUnit;
-
-  @XmlAttribute(name = "mapToUnit", required = true)
-  @XmlSchemaType(name = "positiveInteger")
-  protected BigInteger mapToUnit;
-
-  /**
-   * Gets the value of the mapListFrom property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the mapListFrom property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getMapListFrom().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link MapListType.MapListFrom }
-   * 
-   * 
-   */
-  public List<MapListType.MapListFrom> getMapListFrom()
-  {
-    if (mapListFrom == null)
-    {
-      mapListFrom = new ArrayList<MapListType.MapListFrom>();
-    }
-    return this.mapListFrom;
-  }
-
-  /**
-   * Gets the value of the mapListTo property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the mapListTo property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getMapListTo().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link MapListType.MapListTo }
-   * 
-   * 
-   */
-  public List<MapListType.MapListTo> getMapListTo()
-  {
-    if (mapListTo == null)
-    {
-      mapListTo = new ArrayList<MapListType.MapListTo>();
-    }
-    return this.mapListTo;
-  }
-
-  /**
-   * Gets the value of the mapFromUnit property.
-   * 
-   * @return possible object is {@link BigInteger }
-   * 
-   */
-  public BigInteger getMapFromUnit()
-  {
-    return mapFromUnit;
-  }
-
-  /**
-   * Sets the value of the mapFromUnit property.
-   * 
-   * @param value
-   *          allowed object is {@link BigInteger }
-   * 
-   */
-  public void setMapFromUnit(BigInteger value)
-  {
-    this.mapFromUnit = value;
-  }
+@XmlType(name = "mapListType", propOrder = {
+    "mapListFrom",
+    "mapListTo"
+})
+@XmlSeeAlso({
+    Mapping.class
+})
+public class MapListType {
 
-  /**
-   * Gets the value of the mapToUnit property.
-   * 
-   * @return possible object is {@link BigInteger }
-   * 
-   */
-  public BigInteger getMapToUnit()
-  {
-    return mapToUnit;
-  }
-
-  /**
-   * Sets the value of the mapToUnit property.
-   * 
-   * @param value
-   *          allowed object is {@link BigInteger }
-   * 
-   */
-  public void setMapToUnit(BigInteger value)
-  {
-    this.mapToUnit = value;
-  }
-
-  /**
-   * &lt;p&gt;Java class for anonymous complex type.
-   * 
-   * &lt;p&gt;The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-   * &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
-   * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
-   * /&amp;gt; &amp;lt;attribute name="end" use="required"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
-   * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class MapListFrom
-  {
-
-    @XmlAttribute(name = "start", required = true)
-    protected int start;
-
-    @XmlAttribute(name = "end", required = true)
-    protected int end;
+    protected List<MapListType.MapListFrom> mapListFrom;
+    protected List<MapListType.MapListTo> mapListTo;
+    @XmlAttribute(name = "mapFromUnit", required = true)
+    @XmlSchemaType(name = "positiveInteger")
+    protected BigInteger mapFromUnit;
+    @XmlAttribute(name = "mapToUnit", required = true)
+    @XmlSchemaType(name = "positiveInteger")
+    protected BigInteger mapToUnit;
 
     /**
-     * Gets the value of the start property.
+     * Gets the value of the mapListFrom property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the mapListFrom property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getMapListFrom().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link MapListType.MapListFrom }
+     * 
      * 
      */
-    public int getStart()
-    {
-      return start;
+    public List<MapListType.MapListFrom> getMapListFrom() {
+        if (mapListFrom == null) {
+            mapListFrom = new ArrayList<MapListType.MapListFrom>();
+        }
+        return this.mapListFrom;
     }
 
     /**
-     * Sets the value of the start property.
+     * Gets the value of the mapListTo property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the mapListTo property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getMapListTo().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link MapListType.MapListTo }
+     * 
      * 
      */
-    public void setStart(int value)
-    {
-      this.start = value;
+    public List<MapListType.MapListTo> getMapListTo() {
+        if (mapListTo == null) {
+            mapListTo = new ArrayList<MapListType.MapListTo>();
+        }
+        return this.mapListTo;
     }
 
     /**
-     * Gets the value of the end property.
+     * Gets the value of the mapFromUnit property.
      * 
+     * @return
+     *     possible object is
+     *     {@link BigInteger }
+     *     
      */
-    public int getEnd()
-    {
-      return end;
+    public BigInteger getMapFromUnit() {
+        return mapFromUnit;
     }
 
     /**
-     * Sets the value of the end property.
+     * Sets the value of the mapFromUnit property.
      * 
+     * @param value
+     *     allowed object is
+     *     {@link BigInteger }
+     *     
      */
-    public void setEnd(int value)
-    {
-      this.end = value;
+    public void setMapFromUnit(BigInteger value) {
+        this.mapFromUnit = value;
     }
 
-  }
-
-  /**
-   * &lt;p&gt;Java class for anonymous complex type.
-   * 
-   * &lt;p&gt;The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-   * &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
-   * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
-   * /&amp;gt; &amp;lt;attribute name="end" use="required"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
-   * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class MapListTo
-  {
-
-    @XmlAttribute(name = "start", required = true)
-    protected int start;
-
-    @XmlAttribute(name = "end", required = true)
-    protected int end;
-
     /**
-     * Gets the value of the start property.
+     * Gets the value of the mapToUnit property.
      * 
+     * @return
+     *     possible object is
+     *     {@link BigInteger }
+     *     
      */
-    public int getStart()
-    {
-      return start;
+    public BigInteger getMapToUnit() {
+        return mapToUnit;
     }
 
     /**
-     * Sets the value of the start property.
+     * Sets the value of the mapToUnit property.
      * 
+     * @param value
+     *     allowed object is
+     *     {@link BigInteger }
+     *     
      */
-    public void setStart(int value)
-    {
-      this.start = value;
+    public void setMapToUnit(BigInteger value) {
+        this.mapToUnit = value;
     }
 
+
     /**
-     * Gets the value of the end property.
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
      * 
      */
-    public int getEnd()
-    {
-      return end;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class MapListFrom {
+
+        @XmlAttribute(name = "start", required = true)
+        protected int start;
+        @XmlAttribute(name = "end", required = true)
+        protected int end;
+
+        /**
+         * Gets the value of the start property.
+         * 
+         */
+        public int getStart() {
+            return start;
+        }
+
+        /**
+         * Sets the value of the start property.
+         * 
+         */
+        public void setStart(int value) {
+            this.start = value;
+        }
+
+        /**
+         * Gets the value of the end property.
+         * 
+         */
+        public int getEnd() {
+            return end;
+        }
+
+        /**
+         * Sets the value of the end property.
+         * 
+         */
+        public void setEnd(int value) {
+            this.end = value;
+        }
+
     }
 
+
     /**
-     * Sets the value of the end property.
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
      * 
      */
-    public void setEnd(int value)
-    {
-      this.end = value;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class MapListTo {
 
-  }
+        @XmlAttribute(name = "start", required = true)
+        protected int start;
+        @XmlAttribute(name = "end", required = true)
+        protected int end;
+
+        /**
+         * Gets the value of the start property.
+         * 
+         */
+        public int getStart() {
+            return start;
+        }
+
+        /**
+         * Sets the value of the start property.
+         * 
+         */
+        public void setStart(int value) {
+            this.start = value;
+        }
+
+        /**
+         * Gets the value of the end property.
+         * 
+         */
+        public int getEnd() {
+            return end;
+        }
+
+        /**
+         * Sets the value of the end property.
+         * 
+         */
+        public void setEnd(int value) {
+            this.end = value;
+        }
+
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/Mapping.java b/src/jalview/xml/binding/jalview/Mapping.java
index d79bdee..e898ca2 100644
--- a/src/jalview/xml/binding/jalview/Mapping.java
+++ b/src/jalview/xml/binding/jalview/Mapping.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -14,115 +15,127 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
  * 
- * Represent the jalview.datamodel.Mapping object - it also provides a way of
- * storing sequences that are mapped 'to' without adding them to the sequence
- * set (which will mean they are then added to the alignment too).
- * 
+ * 					Represent the jalview.datamodel.Mapping object - it also provides
+ * 					a way of storing sequences that are mapped 'to' without adding them
+ * 					to the sequence set (which will mean they are then added to the alignment too).
+ * 				
  * 
- * &lt;p&gt;Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
  * 
- * &lt;p&gt;The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
- * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
- * &amp;lt;extension
- * base="{www.vamsas.ac.uk/jalview/version2}mapListType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;choice minOccurs="0"&amp;gt; &amp;lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}Sequence"/&amp;gt; &amp;lt;element
- * name="dseqFor"&amp;gt; &amp;lt;simpleType&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}string"&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/simpleType&amp;gt;
- * &amp;lt;/element&amp;gt; &amp;lt;/choice&amp;gt; &amp;lt;/sequence&amp;gt;
- * &amp;lt;attribute name="mappingType"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;/extension&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
+ * <pre>
+ * &lt;complexType>
+ *   &lt;complexContent>
+ *     &lt;extension base="{www.vamsas.ac.uk/jalview/version2}mapListType">
+ *       &lt;sequence>
+ *         &lt;choice minOccurs="0">
+ *           &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Sequence"/>
+ *           &lt;element name="dseqFor">
+ *             &lt;simpleType>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ *               &lt;/restriction>
+ *             &lt;/simpleType>
+ *           &lt;/element>
+ *         &lt;/choice>
+ *       &lt;/sequence>
+ *       &lt;attribute name="mappingType" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     &lt;/extension>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = { "sequence", "dseqFor" })
+@XmlType(name = "", propOrder = {
+    "sequence",
+    "dseqFor"
+})
 @XmlRootElement(name = "Mapping")
-public class Mapping extends MapListType
+public class Mapping
+    extends MapListType
 {
 
-  @XmlElement(name = "Sequence")
-  protected Sequence sequence;
-
-  protected String dseqFor;
-
-  @XmlAttribute(name = "mappingType")
-  protected String mappingType;
+    @XmlElement(name = "Sequence")
+    protected Sequence sequence;
+    protected String dseqFor;
+    @XmlAttribute(name = "mappingType")
+    protected String mappingType;
 
-  /**
-   * Gets the value of the sequence property.
-   * 
-   * @return possible object is {@link Sequence }
-   * 
-   */
-  public Sequence getSequence()
-  {
-    return sequence;
-  }
+    /**
+     * Gets the value of the sequence property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Sequence }
+     *     
+     */
+    public Sequence getSequence() {
+        return sequence;
+    }
 
-  /**
-   * Sets the value of the sequence property.
-   * 
-   * @param value
-   *          allowed object is {@link Sequence }
-   * 
-   */
-  public void setSequence(Sequence value)
-  {
-    this.sequence = value;
-  }
+    /**
+     * Sets the value of the sequence property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Sequence }
+     *     
+     */
+    public void setSequence(Sequence value) {
+        this.sequence = value;
+    }
 
-  /**
-   * Gets the value of the dseqFor property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDseqFor()
-  {
-    return dseqFor;
-  }
+    /**
+     * Gets the value of the dseqFor property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDseqFor() {
+        return dseqFor;
+    }
 
-  /**
-   * Sets the value of the dseqFor property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDseqFor(String value)
-  {
-    this.dseqFor = value;
-  }
+    /**
+     * Sets the value of the dseqFor property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDseqFor(String value) {
+        this.dseqFor = value;
+    }
 
-  /**
-   * Gets the value of the mappingType property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getMappingType()
-  {
-    return mappingType;
-  }
+    /**
+     * Gets the value of the mappingType property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getMappingType() {
+        return mappingType;
+    }
 
-  /**
-   * Sets the value of the mappingType property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setMappingType(String value)
-  {
-    this.mappingType = value;
-  }
+    /**
+     * Sets the value of the mappingType property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setMappingType(String value) {
+        this.mappingType = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/NoValueColour.java b/src/jalview/xml/binding/jalview/NoValueColour.java
index b0d667c..0eb5a86 100644
--- a/src/jalview/xml/binding/jalview/NoValueColour.java
+++ b/src/jalview/xml/binding/jalview/NoValueColour.java
@@ -1,60 +1,61 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlEnum;
 import javax.xml.bind.annotation.XmlEnumValue;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * &lt;p&gt;Java class for NoValueColour.
+ * <p>Java class for NoValueColour.
  * 
- * &lt;p&gt;The following schema fragment specifies the expected content
- * contained within this class. &lt;pre&gt; &amp;lt;simpleType
- * name="NoValueColour"&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}string"&amp;gt; &amp;lt;enumeration
- * value="None"/&amp;gt; &amp;lt;enumeration value="Min"/&amp;gt;
- * &amp;lt;enumeration value="Max"/&amp;gt; &amp;lt;/restriction&amp;gt;
- * &amp;lt;/simpleType&amp;gt; &lt;/pre&gt;
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * <pre>
+ * &lt;simpleType name="NoValueColour">
+ *   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ *     &lt;enumeration value="None"/>
+ *     &lt;enumeration value="Min"/>
+ *     &lt;enumeration value="Max"/>
+ *   &lt;/restriction>
+ * &lt;/simpleType>
+ * </pre>
  * 
  */
 @XmlType(name = "NoValueColour", namespace = "www.jalview.org/colours")
 @XmlEnum
-public enum NoValueColour
-{
-
-  @XmlEnumValue("None")
-  NONE("None"), @XmlEnumValue("Min")
-  MIN("Min"), @XmlEnumValue("Max")
-  MAX("Max");
-
-  private final String value;
-
-  NoValueColour(String v)
-  {
-    value = v;
-  }
-
-  public String value()
-  {
-    return value;
-  }
-
-  public static NoValueColour fromValue(String v)
-  {
-    for (NoValueColour c : NoValueColour.values())
-    {
-      if (c.value.equals(v))
-      {
-        return c;
-      }
+public enum NoValueColour {
+
+    @XmlEnumValue("None")
+    NONE("None"),
+    @XmlEnumValue("Min")
+    MIN("Min"),
+    @XmlEnumValue("Max")
+    MAX("Max");
+    private final String value;
+
+    NoValueColour(String v) {
+        value = v;
+    }
+
+    public String value() {
+        return value;
+    }
+
+    public static NoValueColour fromValue(String v) {
+        for (NoValueColour c: NoValueColour.values()) {
+            if (c.value.equals(v)) {
+                return c;
+            }
+        }
+        throw new IllegalArgumentException(v);
     }
-    throw new IllegalArgumentException(v);
-  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/ObjectFactory.java b/src/jalview/xml/binding/jalview/ObjectFactory.java
index 46ae594..8b38877 100644
--- a/src/jalview/xml/binding/jalview/ObjectFactory.java
+++ b/src/jalview/xml/binding/jalview/ObjectFactory.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.JAXBElement;
@@ -12,560 +13,484 @@ import javax.xml.bind.annotation.XmlElementDecl;
 import javax.xml.bind.annotation.XmlRegistry;
 import javax.xml.namespace.QName;
 
+
 /**
- * This object contains factory methods for each Java content interface and Java
- * element interface generated in the jalview.xml.binding.jalview package.
- * &lt;p&gt;An ObjectFactory allows you to programatically construct new
- * instances of the Java representation for XML content. The Java representation
- * of XML content can consist of schema derived interfaces and classes
- * representing the binding of schema type definitions, element declarations and
- * model groups. Factory methods for each of these are provided in this class.
+ * This object contains factory methods for each 
+ * Java content interface and Java element interface 
+ * generated in the jalview.xml.binding.jalview package. 
+ * <p>An ObjectFactory allows you to programatically 
+ * construct new instances of the Java representation 
+ * for XML content. The Java representation of XML 
+ * content can consist of schema derived interfaces 
+ * and classes representing the binding of schema 
+ * type definitions, element declarations and model 
+ * groups.  Factory methods for each of these are 
+ * provided in this class.
  * 
  */
 @XmlRegistry
-public class ObjectFactory
-{
-
-  private final static QName _JalviewModel_QNAME = new QName(
-          "www.jalview.org", "JalviewModel");
-
-  private final static QName _JalviewUserColours_QNAME = new QName(
-          "www.jalview.org/colours", "JalviewUserColours");
-
-  private final static QName _WebServiceParameterSet_QNAME = new QName(
-          "www.jalview.org/xml/wsparamset", "WebServiceParameterSet");
-
-  /**
-   * Create a new ObjectFactory that can be used to create new instances of
-   * schema derived classes for package: jalview.xml.binding.jalview
-   * 
-   */
-  public ObjectFactory()
-  {
-  }
-
-  /**
-   * Create an instance of {@link MapListType }
-   * 
-   */
-  public MapListType createMapListType()
-  {
-    return new MapListType();
-  }
-
-  /**
-   * Create an instance of {@link Sequence }
-   * 
-   */
-  public Sequence createSequence()
-  {
-    return new Sequence();
-  }
-
-  /**
-   * Create an instance of {@link AlcodonFrame }
-   * 
-   */
-  public AlcodonFrame createAlcodonFrame()
-  {
-    return new AlcodonFrame();
-  }
-
-  /**
-   * Create an instance of {@link Annotation }
-   * 
-   */
-  public Annotation createAnnotation()
-  {
-    return new Annotation();
-  }
-
-  /**
-   * Create an instance of {@link SequenceSet }
-   * 
-   */
-  public SequenceSet createSequenceSet()
-  {
-    return new SequenceSet();
-  }
-
-  /**
-   * Create an instance of {@link FeatureMatcherSet }
-   * 
-   */
-  public FeatureMatcherSet createFeatureMatcherSet()
-  {
-    return new FeatureMatcherSet();
-  }
-
-  /**
-   * Create an instance of {@link JalviewUserColours }
-   * 
-   */
-  public JalviewUserColours createJalviewUserColours()
-  {
-    return new JalviewUserColours();
-  }
-
-  /**
-   * Create an instance of {@link Pdbentry }
-   * 
-   */
-  public Pdbentry createPdbentry()
-  {
-    return new Pdbentry();
-  }
-
-  /**
-   * Create an instance of {@link Feature }
-   * 
-   */
-  public Feature createFeature()
-  {
-    return new Feature();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel }
-   * 
-   */
-  public JalviewModel createJalviewModel()
-  {
-    return new JalviewModel();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.FeatureSettings }
-   * 
-   */
-  public JalviewModel.FeatureSettings createJalviewModelFeatureSettings()
-  {
-    return new JalviewModel.FeatureSettings();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.PcaViewer }
-   * 
-   */
-  public JalviewModel.PcaViewer createJalviewModelPcaViewer()
-  {
-    return new JalviewModel.PcaViewer();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.Viewport }
-   * 
-   */
-  public JalviewModel.Viewport createJalviewModelViewport()
-  {
-    return new JalviewModel.Viewport();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.JSeq }
-   * 
-   */
-  public JalviewModel.JSeq createJalviewModelJSeq()
-  {
-    return new JalviewModel.JSeq();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.JSeq.RnaViewer }
-   * 
-   */
-  public JalviewModel.JSeq.RnaViewer createJalviewModelJSeqRnaViewer()
-  {
-    return new JalviewModel.JSeq.RnaViewer();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.JSeq.Pdbids }
-   * 
-   */
-  public JalviewModel.JSeq.Pdbids createJalviewModelJSeqPdbids()
-  {
-    return new JalviewModel.JSeq.Pdbids();
-  }
-
-  /**
-   * Create an instance of {@link AnnotationColourScheme }
-   * 
-   */
-  public AnnotationColourScheme createAnnotationColourScheme()
-  {
-    return new AnnotationColourScheme();
-  }
-
-  /**
-   * Create an instance of {@link PcaDataType }
-   * 
-   */
-  public PcaDataType createPcaDataType()
-  {
-    return new PcaDataType();
-  }
-
-  /**
-   * Create an instance of {@link DoubleVector }
-   * 
-   */
-  public DoubleVector createDoubleVector()
-  {
-    return new DoubleVector();
-  }
-
-  /**
-   * Create an instance of {@link DoubleMatrix }
-   * 
-   */
-  public DoubleMatrix createDoubleMatrix()
-  {
-    return new DoubleMatrix();
-  }
-
-  /**
-   * Create an instance of {@link Mapping }
-   * 
-   */
-  public Mapping createMapping()
-  {
-    return new Mapping();
-  }
-
-  /**
-   * Create an instance of {@link MapListType.MapListFrom }
-   * 
-   */
-  public MapListType.MapListFrom createMapListTypeMapListFrom()
-  {
-    return new MapListType.MapListFrom();
-  }
-
-  /**
-   * Create an instance of {@link MapListType.MapListTo }
-   * 
-   */
-  public MapListType.MapListTo createMapListTypeMapListTo()
-  {
-    return new MapListType.MapListTo();
-  }
-
-  /**
-   * Create an instance of {@link SequenceType }
-   * 
-   */
-  public SequenceType createSequenceType()
-  {
-    return new SequenceType();
-  }
-
-  /**
-   * Create an instance of {@link Sequence.DBRef }
-   * 
-   */
-  public Sequence.DBRef createSequenceDBRef()
-  {
-    return new Sequence.DBRef();
-  }
-
-  /**
-   * Create an instance of {@link AlcodonFrame.Alcodon }
-   * 
-   */
-  public AlcodonFrame.Alcodon createAlcodonFrameAlcodon()
-  {
-    return new AlcodonFrame.Alcodon();
-  }
-
-  /**
-   * Create an instance of {@link AlcodonFrame.AlcodMap }
-   * 
-   */
-  public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap()
-  {
-    return new AlcodonFrame.AlcodMap();
-  }
-
-  /**
-   * Create an instance of {@link AnnotationElement }
-   * 
-   */
-  public AnnotationElement createAnnotationElement()
-  {
-    return new AnnotationElement();
-  }
-
-  /**
-   * Create an instance of {@link Annotation.ThresholdLine }
-   * 
-   */
-  public Annotation.ThresholdLine createAnnotationThresholdLine()
-  {
-    return new Annotation.ThresholdLine();
-  }
-
-  /**
-   * Create an instance of {@link Annotation.Property }
-   * 
-   */
-  public Annotation.Property createAnnotationProperty()
-  {
-    return new Annotation.Property();
-  }
-
-  /**
-   * Create an instance of {@link SequenceSet.SequenceSetProperties }
-   * 
-   */
-  public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties()
-  {
-    return new SequenceSet.SequenceSetProperties();
-  }
-
-  /**
-   * Create an instance of {@link VAMSAS }
-   * 
-   */
-  public VAMSAS createVAMSAS()
-  {
-    return new VAMSAS();
-  }
-
-  /**
-   * Create an instance of {@link FeatureMatcher }
-   * 
-   */
-  public FeatureMatcher createFeatureMatcher()
-  {
-    return new FeatureMatcher();
-  }
-
-  /**
-   * Create an instance of {@link WebServiceParameterSet }
-   * 
-   */
-  public WebServiceParameterSet createWebServiceParameterSet()
-  {
-    return new WebServiceParameterSet();
-  }
-
-  /**
-   * Create an instance of {@link FeatureMatcherSet.CompoundMatcher }
-   * 
-   */
-  public FeatureMatcherSet.CompoundMatcher createFeatureMatcherSetCompoundMatcher()
-  {
-    return new FeatureMatcherSet.CompoundMatcher();
-  }
-
-  /**
-   * Create an instance of {@link JalviewUserColours.Colour }
-   * 
-   */
-  public JalviewUserColours.Colour createJalviewUserColoursColour()
-  {
-    return new JalviewUserColours.Colour();
-  }
-
-  /**
-   * Create an instance of {@link JalviewUserColours.Filter }
-   * 
-   */
-  public JalviewUserColours.Filter createJalviewUserColoursFilter()
-  {
-    return new JalviewUserColours.Filter();
-  }
-
-  /**
-   * Create an instance of {@link Pdbentry.Property }
-   * 
-   */
-  public Pdbentry.Property createPdbentryProperty()
-  {
-    return new Pdbentry.Property();
-  }
-
-  /**
-   * Create an instance of {@link Feature.OtherData }
-   * 
-   */
-  public Feature.OtherData createFeatureOtherData()
-  {
-    return new Feature.OtherData();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.JGroup }
-   * 
-   */
-  public JalviewModel.JGroup createJalviewModelJGroup()
-  {
-    return new JalviewModel.JGroup();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.UserColours }
-   * 
-   */
-  public JalviewModel.UserColours createJalviewModelUserColours()
-  {
-    return new JalviewModel.UserColours();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.Tree }
-   * 
-   */
-  public JalviewModel.Tree createJalviewModelTree()
-  {
-    return new JalviewModel.Tree();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.FeatureSettings.Setting }
-   * 
-   */
-  public JalviewModel.FeatureSettings.Setting createJalviewModelFeatureSettingsSetting()
-  {
-    return new JalviewModel.FeatureSettings.Setting();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.FeatureSettings.Group }
-   * 
-   */
-  public JalviewModel.FeatureSettings.Group createJalviewModelFeatureSettingsGroup()
-  {
-    return new JalviewModel.FeatureSettings.Group();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.PcaViewer.SequencePoint }
-   * 
-   */
-  public JalviewModel.PcaViewer.SequencePoint createJalviewModelPcaViewerSequencePoint()
-  {
-    return new JalviewModel.PcaViewer.SequencePoint();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.PcaViewer.Axis }
-   * 
-   */
-  public JalviewModel.PcaViewer.Axis createJalviewModelPcaViewerAxis()
-  {
-    return new JalviewModel.PcaViewer.Axis();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMin }
-   * 
-   */
-  public JalviewModel.PcaViewer.SeqPointMin createJalviewModelPcaViewerSeqPointMin()
-  {
-    return new JalviewModel.PcaViewer.SeqPointMin();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMax }
-   * 
-   */
-  public JalviewModel.PcaViewer.SeqPointMax createJalviewModelPcaViewerSeqPointMax()
-  {
-    return new JalviewModel.PcaViewer.SeqPointMax();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.Viewport.HiddenColumns }
-   * 
-   */
-  public JalviewModel.Viewport.HiddenColumns createJalviewModelViewportHiddenColumns()
-  {
-    return new JalviewModel.Viewport.HiddenColumns();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.Viewport.CalcIdParam }
-   * 
-   */
-  public JalviewModel.Viewport.CalcIdParam createJalviewModelViewportCalcIdParam()
-  {
-    return new JalviewModel.Viewport.CalcIdParam();
-  }
-
-  /**
-   * Create an instance of
-   * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
-   * 
-   */
-  public JalviewModel.JSeq.RnaViewer.SecondaryStructure createJalviewModelJSeqRnaViewerSecondaryStructure()
-  {
-    return new JalviewModel.JSeq.RnaViewer.SecondaryStructure();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.JSeq.Pdbids.StructureState }
-   * 
-   */
-  public JalviewModel.JSeq.Pdbids.StructureState createJalviewModelJSeqPdbidsStructureState()
-  {
-    return new JalviewModel.JSeq.Pdbids.StructureState();
-  }
-
-  /**
-   * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel
-   * }{@code >}
-   * 
-   * @param value
-   *          Java instance representing xml element's value.
-   * @return the new instance of {@link JAXBElement
-   *         }{@code <}{@link JalviewModel }{@code >}
-   */
-  @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
-  public JAXBElement<JalviewModel> createJalviewModel(JalviewModel value)
-  {
-    return new JAXBElement<JalviewModel>(_JalviewModel_QNAME,
-            JalviewModel.class, null, value);
-  }
-
-  /**
-   * Create an instance of {@link JAXBElement
-   * }{@code <}{@link JalviewUserColours }{@code >}
-   * 
-   * @param value
-   *          Java instance representing xml element's value.
-   * @return the new instance of {@link JAXBElement
-   *         }{@code <}{@link JalviewUserColours }{@code >}
-   */
-  @XmlElementDecl(
-    namespace = "www.jalview.org/colours",
-    name = "JalviewUserColours")
-  public JAXBElement<JalviewUserColours> createJalviewUserColours(
-          JalviewUserColours value)
-  {
-    return new JAXBElement<JalviewUserColours>(_JalviewUserColours_QNAME,
-            JalviewUserColours.class, null, value);
-  }
-
-  /**
-   * Create an instance of {@link JAXBElement
-   * }{@code <}{@link WebServiceParameterSet }{@code >}
-   * 
-   * @param value
-   *          Java instance representing xml element's value.
-   * @return the new instance of {@link JAXBElement
-   *         }{@code <}{@link WebServiceParameterSet }{@code >}
-   */
-  @XmlElementDecl(
-    namespace = "www.jalview.org/xml/wsparamset",
-    name = "WebServiceParameterSet")
-  public JAXBElement<WebServiceParameterSet> createWebServiceParameterSet(
-          WebServiceParameterSet value)
-  {
-    return new JAXBElement<WebServiceParameterSet>(
-            _WebServiceParameterSet_QNAME, WebServiceParameterSet.class,
-            null, value);
-  }
+public class ObjectFactory {
+
+    private final static QName _WebServiceParameterSet_QNAME = new QName("www.jalview.org/xml/wsparamset", "WebServiceParameterSet");
+    private final static QName _JalviewModel_QNAME = new QName("www.jalview.org", "JalviewModel");
+    private final static QName _JalviewUserColours_QNAME = new QName("www.jalview.org/colours", "JalviewUserColours");
+
+    /**
+     * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.jalview
+     * 
+     */
+    public ObjectFactory() {
+    }
+
+    /**
+     * Create an instance of {@link AlcodonFrame }
+     * 
+     */
+    public AlcodonFrame createAlcodonFrame() {
+        return new AlcodonFrame();
+    }
+
+    /**
+     * Create an instance of {@link MapListType }
+     * 
+     */
+    public MapListType createMapListType() {
+        return new MapListType();
+    }
+
+    /**
+     * Create an instance of {@link Sequence }
+     * 
+     */
+    public Sequence createSequence() {
+        return new Sequence();
+    }
+
+    /**
+     * Create an instance of {@link Annotation }
+     * 
+     */
+    public Annotation createAnnotation() {
+        return new Annotation();
+    }
+
+    /**
+     * Create an instance of {@link SequenceSet }
+     * 
+     */
+    public SequenceSet createSequenceSet() {
+        return new SequenceSet();
+    }
+
+    /**
+     * Create an instance of {@link FeatureMatcherSet }
+     * 
+     */
+    public FeatureMatcherSet createFeatureMatcherSet() {
+        return new FeatureMatcherSet();
+    }
+
+    /**
+     * Create an instance of {@link JalviewUserColours }
+     * 
+     */
+    public JalviewUserColours createJalviewUserColours() {
+        return new JalviewUserColours();
+    }
+
+    /**
+     * Create an instance of {@link Pdbentry }
+     * 
+     */
+    public Pdbentry createPdbentry() {
+        return new Pdbentry();
+    }
+
+    /**
+     * Create an instance of {@link Feature }
+     * 
+     */
+    public Feature createFeature() {
+        return new Feature();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel }
+     * 
+     */
+    public JalviewModel createJalviewModel() {
+        return new JalviewModel();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.FeatureSettings }
+     * 
+     */
+    public JalviewModel.FeatureSettings createJalviewModelFeatureSettings() {
+        return new JalviewModel.FeatureSettings();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.PcaViewer }
+     * 
+     */
+    public JalviewModel.PcaViewer createJalviewModelPcaViewer() {
+        return new JalviewModel.PcaViewer();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.Viewport }
+     * 
+     */
+    public JalviewModel.Viewport createJalviewModelViewport() {
+        return new JalviewModel.Viewport();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.JSeq }
+     * 
+     */
+    public JalviewModel.JSeq createJalviewModelJSeq() {
+        return new JalviewModel.JSeq();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.JSeq.RnaViewer }
+     * 
+     */
+    public JalviewModel.JSeq.RnaViewer createJalviewModelJSeqRnaViewer() {
+        return new JalviewModel.JSeq.RnaViewer();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.JSeq.Pdbids }
+     * 
+     */
+    public JalviewModel.JSeq.Pdbids createJalviewModelJSeqPdbids() {
+        return new JalviewModel.JSeq.Pdbids();
+    }
+
+    /**
+     * Create an instance of {@link DoubleMatrix }
+     * 
+     */
+    public DoubleMatrix createDoubleMatrix() {
+        return new DoubleMatrix();
+    }
+
+    /**
+     * Create an instance of {@link AnnotationColourScheme }
+     * 
+     */
+    public AnnotationColourScheme createAnnotationColourScheme() {
+        return new AnnotationColourScheme();
+    }
+
+    /**
+     * Create an instance of {@link PcaDataType }
+     * 
+     */
+    public PcaDataType createPcaDataType() {
+        return new PcaDataType();
+    }
+
+    /**
+     * Create an instance of {@link DoubleVector }
+     * 
+     */
+    public DoubleVector createDoubleVector() {
+        return new DoubleVector();
+    }
+
+    /**
+     * Create an instance of {@link AlcodonFrame.Alcodon }
+     * 
+     */
+    public AlcodonFrame.Alcodon createAlcodonFrameAlcodon() {
+        return new AlcodonFrame.Alcodon();
+    }
+
+    /**
+     * Create an instance of {@link AlcodonFrame.AlcodMap }
+     * 
+     */
+    public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap() {
+        return new AlcodonFrame.AlcodMap();
+    }
+
+    /**
+     * Create an instance of {@link AnnotationElement }
+     * 
+     */
+    public AnnotationElement createAnnotationElement() {
+        return new AnnotationElement();
+    }
+
+    /**
+     * Create an instance of {@link Mapping }
+     * 
+     */
+    public Mapping createMapping() {
+        return new Mapping();
+    }
+
+    /**
+     * Create an instance of {@link MapListType.MapListFrom }
+     * 
+     */
+    public MapListType.MapListFrom createMapListTypeMapListFrom() {
+        return new MapListType.MapListFrom();
+    }
+
+    /**
+     * Create an instance of {@link MapListType.MapListTo }
+     * 
+     */
+    public MapListType.MapListTo createMapListTypeMapListTo() {
+        return new MapListType.MapListTo();
+    }
+
+    /**
+     * Create an instance of {@link SequenceType }
+     * 
+     */
+    public SequenceType createSequenceType() {
+        return new SequenceType();
+    }
+
+    /**
+     * Create an instance of {@link Sequence.DBRef }
+     * 
+     */
+    public Sequence.DBRef createSequenceDBRef() {
+        return new Sequence.DBRef();
+    }
+
+    /**
+     * Create an instance of {@link Annotation.ThresholdLine }
+     * 
+     */
+    public Annotation.ThresholdLine createAnnotationThresholdLine() {
+        return new Annotation.ThresholdLine();
+    }
+
+    /**
+     * Create an instance of {@link Annotation.Property }
+     * 
+     */
+    public Annotation.Property createAnnotationProperty() {
+        return new Annotation.Property();
+    }
+
+    /**
+     * Create an instance of {@link SequenceSet.SequenceSetProperties }
+     * 
+     */
+    public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties() {
+        return new SequenceSet.SequenceSetProperties();
+    }
+
+    /**
+     * Create an instance of {@link VAMSAS }
+     * 
+     */
+    public VAMSAS createVAMSAS() {
+        return new VAMSAS();
+    }
+
+    /**
+     * Create an instance of {@link FeatureMatcher }
+     * 
+     */
+    public FeatureMatcher createFeatureMatcher() {
+        return new FeatureMatcher();
+    }
+
+    /**
+     * Create an instance of {@link WebServiceParameterSet }
+     * 
+     */
+    public WebServiceParameterSet createWebServiceParameterSet() {
+        return new WebServiceParameterSet();
+    }
+
+    /**
+     * Create an instance of {@link FeatureMatcherSet.CompoundMatcher }
+     * 
+     */
+    public FeatureMatcherSet.CompoundMatcher createFeatureMatcherSetCompoundMatcher() {
+        return new FeatureMatcherSet.CompoundMatcher();
+    }
+
+    /**
+     * Create an instance of {@link JalviewUserColours.Colour }
+     * 
+     */
+    public JalviewUserColours.Colour createJalviewUserColoursColour() {
+        return new JalviewUserColours.Colour();
+    }
+
+    /**
+     * Create an instance of {@link JalviewUserColours.Filter }
+     * 
+     */
+    public JalviewUserColours.Filter createJalviewUserColoursFilter() {
+        return new JalviewUserColours.Filter();
+    }
+
+    /**
+     * Create an instance of {@link Pdbentry.Property }
+     * 
+     */
+    public Pdbentry.Property createPdbentryProperty() {
+        return new Pdbentry.Property();
+    }
+
+    /**
+     * Create an instance of {@link Feature.OtherData }
+     * 
+     */
+    public Feature.OtherData createFeatureOtherData() {
+        return new Feature.OtherData();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.JGroup }
+     * 
+     */
+    public JalviewModel.JGroup createJalviewModelJGroup() {
+        return new JalviewModel.JGroup();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.UserColours }
+     * 
+     */
+    public JalviewModel.UserColours createJalviewModelUserColours() {
+        return new JalviewModel.UserColours();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.Tree }
+     * 
+     */
+    public JalviewModel.Tree createJalviewModelTree() {
+        return new JalviewModel.Tree();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.FeatureSettings.Setting }
+     * 
+     */
+    public JalviewModel.FeatureSettings.Setting createJalviewModelFeatureSettingsSetting() {
+        return new JalviewModel.FeatureSettings.Setting();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.FeatureSettings.Group }
+     * 
+     */
+    public JalviewModel.FeatureSettings.Group createJalviewModelFeatureSettingsGroup() {
+        return new JalviewModel.FeatureSettings.Group();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.PcaViewer.SequencePoint }
+     * 
+     */
+    public JalviewModel.PcaViewer.SequencePoint createJalviewModelPcaViewerSequencePoint() {
+        return new JalviewModel.PcaViewer.SequencePoint();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.PcaViewer.Axis }
+     * 
+     */
+    public JalviewModel.PcaViewer.Axis createJalviewModelPcaViewerAxis() {
+        return new JalviewModel.PcaViewer.Axis();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMin }
+     * 
+     */
+    public JalviewModel.PcaViewer.SeqPointMin createJalviewModelPcaViewerSeqPointMin() {
+        return new JalviewModel.PcaViewer.SeqPointMin();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMax }
+     * 
+     */
+    public JalviewModel.PcaViewer.SeqPointMax createJalviewModelPcaViewerSeqPointMax() {
+        return new JalviewModel.PcaViewer.SeqPointMax();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.Viewport.HiddenColumns }
+     * 
+     */
+    public JalviewModel.Viewport.HiddenColumns createJalviewModelViewportHiddenColumns() {
+        return new JalviewModel.Viewport.HiddenColumns();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.Viewport.CalcIdParam }
+     * 
+     */
+    public JalviewModel.Viewport.CalcIdParam createJalviewModelViewportCalcIdParam() {
+        return new JalviewModel.Viewport.CalcIdParam();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.Viewport.Overview }
+     * 
+     */
+    public JalviewModel.Viewport.Overview createJalviewModelViewportOverview() {
+        return new JalviewModel.Viewport.Overview();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
+     * 
+     */
+    public JalviewModel.JSeq.RnaViewer.SecondaryStructure createJalviewModelJSeqRnaViewerSecondaryStructure() {
+        return new JalviewModel.JSeq.RnaViewer.SecondaryStructure();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.JSeq.Pdbids.StructureState }
+     * 
+     */
+    public JalviewModel.JSeq.Pdbids.StructureState createJalviewModelJSeqPdbidsStructureState() {
+        return new JalviewModel.JSeq.Pdbids.StructureState();
+    }
+
+    /**
+     * Create an instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}}
+     * 
+     */
+    @XmlElementDecl(namespace = "www.jalview.org/xml/wsparamset", name = "WebServiceParameterSet")
+    public JAXBElement<WebServiceParameterSet> createWebServiceParameterSet(WebServiceParameterSet value) {
+        return new JAXBElement<WebServiceParameterSet>(_WebServiceParameterSet_QNAME, WebServiceParameterSet.class, null, value);
+    }
+
+    /**
+     * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}}
+     * 
+     */
+    @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
+    public JAXBElement<JalviewModel> createJalviewModel(JalviewModel value) {
+        return new JAXBElement<JalviewModel>(_JalviewModel_QNAME, JalviewModel.class, null, value);
+    }
+
+    /**
+     * Create an instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}}
+     * 
+     */
+    @XmlElementDecl(namespace = "www.jalview.org/colours", name = "JalviewUserColours")
+    public JAXBElement<JalviewUserColours> createJalviewUserColours(JalviewUserColours value) {
+        return new JAXBElement<JalviewUserColours>(_JalviewUserColours_QNAME, JalviewUserColours.class, null, value);
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/PcaDataType.java b/src/jalview/xml/binding/jalview/PcaDataType.java
index 0717541..b261199 100644
--- a/src/jalview/xml/binding/jalview/PcaDataType.java
+++ b/src/jalview/xml/binding/jalview/PcaDataType.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,114 +13,117 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
  * 
- * The results of a PCA calculation
- * 
+ * 				The results of a PCA calculation
+ * 			
  * 
- * &lt;p&gt;Java class for PcaDataType complex type.
+ * <p>Java class for PcaDataType complex type.
  * 
- * &lt;p&gt;The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
- * &lt;pre&gt; &amp;lt;complexType name="PcaDataType"&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="pairwiseMatrix"
- * type="{www.jalview.org}DoubleMatrix"/&amp;gt; &amp;lt;element
- * name="tridiagonalMatrix" type="{www.jalview.org}DoubleMatrix"/&amp;gt;
- * &amp;lt;element name="eigenMatrix"
- * type="{www.jalview.org}DoubleMatrix"/&amp;gt; &amp;lt;/sequence&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
+ * <pre>
+ * &lt;complexType name="PcaDataType">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="pairwiseMatrix" type="{www.jalview.org}DoubleMatrix"/>
+ *         &lt;element name="tridiagonalMatrix" type="{www.jalview.org}DoubleMatrix"/>
+ *         &lt;element name="eigenMatrix" type="{www.jalview.org}DoubleMatrix"/>
+ *       &lt;/sequence>
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "PcaDataType",
-  namespace = "www.jalview.org",
-  propOrder =
-  { "pairwiseMatrix", "tridiagonalMatrix", "eigenMatrix" })
-public class PcaDataType
-{
-
-  @XmlElement(required = true)
-  protected DoubleMatrix pairwiseMatrix;
-
-  @XmlElement(required = true)
-  protected DoubleMatrix tridiagonalMatrix;
+@XmlType(name = "PcaDataType", namespace = "www.jalview.org", propOrder = {
+    "pairwiseMatrix",
+    "tridiagonalMatrix",
+    "eigenMatrix"
+})
+public class PcaDataType {
 
-  @XmlElement(required = true)
-  protected DoubleMatrix eigenMatrix;
+    @XmlElement(required = true)
+    protected DoubleMatrix pairwiseMatrix;
+    @XmlElement(required = true)
+    protected DoubleMatrix tridiagonalMatrix;
+    @XmlElement(required = true)
+    protected DoubleMatrix eigenMatrix;
 
-  /**
-   * Gets the value of the pairwiseMatrix property.
-   * 
-   * @return possible object is {@link DoubleMatrix }
-   * 
-   */
-  public DoubleMatrix getPairwiseMatrix()
-  {
-    return pairwiseMatrix;
-  }
+    /**
+     * Gets the value of the pairwiseMatrix property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link DoubleMatrix }
+     *     
+     */
+    public DoubleMatrix getPairwiseMatrix() {
+        return pairwiseMatrix;
+    }
 
-  /**
-   * Sets the value of the pairwiseMatrix property.
-   * 
-   * @param value
-   *          allowed object is {@link DoubleMatrix }
-   * 
-   */
-  public void setPairwiseMatrix(DoubleMatrix value)
-  {
-    this.pairwiseMatrix = value;
-  }
+    /**
+     * Sets the value of the pairwiseMatrix property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link DoubleMatrix }
+     *     
+     */
+    public void setPairwiseMatrix(DoubleMatrix value) {
+        this.pairwiseMatrix = value;
+    }
 
-  /**
-   * Gets the value of the tridiagonalMatrix property.
-   * 
-   * @return possible object is {@link DoubleMatrix }
-   * 
-   */
-  public DoubleMatrix getTridiagonalMatrix()
-  {
-    return tridiagonalMatrix;
-  }
+    /**
+     * Gets the value of the tridiagonalMatrix property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link DoubleMatrix }
+     *     
+     */
+    public DoubleMatrix getTridiagonalMatrix() {
+        return tridiagonalMatrix;
+    }
 
-  /**
-   * Sets the value of the tridiagonalMatrix property.
-   * 
-   * @param value
-   *          allowed object is {@link DoubleMatrix }
-   * 
-   */
-  public void setTridiagonalMatrix(DoubleMatrix value)
-  {
-    this.tridiagonalMatrix = value;
-  }
+    /**
+     * Sets the value of the tridiagonalMatrix property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link DoubleMatrix }
+     *     
+     */
+    public void setTridiagonalMatrix(DoubleMatrix value) {
+        this.tridiagonalMatrix = value;
+    }
 
-  /**
-   * Gets the value of the eigenMatrix property.
-   * 
-   * @return possible object is {@link DoubleMatrix }
-   * 
-   */
-  public DoubleMatrix getEigenMatrix()
-  {
-    return eigenMatrix;
-  }
+    /**
+     * Gets the value of the eigenMatrix property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link DoubleMatrix }
+     *     
+     */
+    public DoubleMatrix getEigenMatrix() {
+        return eigenMatrix;
+    }
 
-  /**
-   * Sets the value of the eigenMatrix property.
-   * 
-   * @param value
-   *          allowed object is {@link DoubleMatrix }
-   * 
-   */
-  public void setEigenMatrix(DoubleMatrix value)
-  {
-    this.eigenMatrix = value;
-  }
+    /**
+     * Sets the value of the eigenMatrix property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link DoubleMatrix }
+     *     
+     */
+    public void setEigenMatrix(DoubleMatrix value) {
+        this.eigenMatrix = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/Pdbentry.java b/src/jalview/xml/binding/jalview/Pdbentry.java
index 7d5447b..fd2e336 100644
--- a/src/jalview/xml/binding/jalview/Pdbentry.java
+++ b/src/jalview/xml/binding/jalview/Pdbentry.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -15,223 +16,232 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlSeeAlso;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * &lt;p&gt;Java class for pdbentry complex type.
+ * <p>Java class for pdbentry complex type.
  * 
- * &lt;p&gt;The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
- * &lt;pre&gt; &amp;lt;complexType name="pdbentry"&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;sequence
- * maxOccurs="unbounded" minOccurs="0"&amp;gt; &amp;lt;element name="property"
- * maxOccurs="unbounded" minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
- * name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&amp;gt; &amp;lt;attribute name="value" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
- * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="id" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
- * name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;attribute name="file" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&amp;gt; &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
+ * <pre>
+ * &lt;complexType name="pdbentry">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence maxOccurs="unbounded" minOccurs="0">
+ *         &lt;element name="property" maxOccurs="unbounded" minOccurs="0">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *       &lt;/sequence>
+ *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="file" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "pdbentry",
-  namespace = "www.jalview.org",
-  propOrder =
-  { "property" })
-@XmlSeeAlso({ jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.class })
-public class Pdbentry
-{
-
-  protected List<Pdbentry.Property> property;
-
-  @XmlAttribute(name = "id", required = true)
-  protected String id;
-
-  @XmlAttribute(name = "type")
-  protected String type;
-
-  @XmlAttribute(name = "file")
-  protected String file;
-
-  /**
-   * Gets the value of the property property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the property property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getProperty().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link Pdbentry.Property }
-   * 
-   * 
-   */
-  public List<Pdbentry.Property> getProperty()
-  {
-    if (property == null)
-    {
-      property = new ArrayList<Pdbentry.Property>();
-    }
-    return this.property;
-  }
-
-  /**
-   * Gets the value of the id property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getId()
-  {
-    return id;
-  }
-
-  /**
-   * Sets the value of the id property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setId(String value)
-  {
-    this.id = value;
-  }
-
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
-
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
-
-  /**
-   * Gets the value of the file property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getFile()
-  {
-    return file;
-  }
-
-  /**
-   * Sets the value of the file property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setFile(String value)
-  {
-    this.file = value;
-  }
-
-  /**
-   * &lt;p&gt;Java class for anonymous complex type.
-   * 
-   * &lt;p&gt;The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-   * &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
-   * name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
-   * /&amp;gt; &amp;lt;attribute name="value" use="required"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-   * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class Property
-  {
-
-    @XmlAttribute(name = "name", required = true)
-    protected String name;
-
-    @XmlAttribute(name = "value", required = true)
-    protected String value;
+@XmlType(name = "pdbentry", namespace = "www.jalview.org", propOrder = {
+    "property"
+})
+@XmlSeeAlso({
+    jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.class
+})
+public class Pdbentry {
+
+    protected List<Pdbentry.Property> property;
+    @XmlAttribute(name = "id", required = true)
+    protected String id;
+    @XmlAttribute(name = "type")
+    protected String type;
+    @XmlAttribute(name = "file")
+    protected String file;
 
     /**
-     * Gets the value of the name property.
+     * Gets the value of the property property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the property property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getProperty().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link Pdbentry.Property }
+     * 
      * 
-     * @return possible object is {@link String }
+     */
+    public List<Pdbentry.Property> getProperty() {
+        if (property == null) {
+            property = new ArrayList<Pdbentry.Property>();
+        }
+        return this.property;
+    }
+
+    /**
+     * Gets the value of the id property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getName()
-    {
-      return name;
+    public String getId() {
+        return id;
     }
 
     /**
-     * Sets the value of the name property.
+     * Sets the value of the id property.
      * 
      * @param value
-     *          allowed object is {@link String }
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setId(String value) {
+        this.id = value;
+    }
+
+    /**
+     * Gets the value of the type property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public void setName(String value)
-    {
-      this.name = value;
+    public String getType() {
+        return type;
     }
 
     /**
-     * Gets the value of the value property.
+     * Sets the value of the type property.
      * 
-     * @return possible object is {@link String }
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
+
+    /**
+     * Gets the value of the file property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getValue()
-    {
-      return value;
+    public String getFile() {
+        return file;
     }
 
     /**
-     * Sets the value of the value property.
+     * Sets the value of the file property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setValue(String value)
-    {
-      this.value = value;
+    public void setFile(String value) {
+        this.file = value;
     }
 
-  }
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class Property {
+
+        @XmlAttribute(name = "name", required = true)
+        protected String name;
+        @XmlAttribute(name = "value", required = true)
+        protected String value;
+
+        /**
+         * Gets the value of the name property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getName() {
+            return name;
+        }
+
+        /**
+         * Sets the value of the name property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setName(String value) {
+            this.name = value;
+        }
+
+        /**
+         * Gets the value of the value property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getValue() {
+            return value;
+        }
+
+        /**
+         * Sets the value of the value property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setValue(String value) {
+            this.value = value;
+        }
+
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/Sequence.java b/src/jalview/xml/binding/jalview/Sequence.java
index 2001845..6a199a2 100644
--- a/src/jalview/xml/binding/jalview/Sequence.java
+++ b/src/jalview/xml/binding/jalview/Sequence.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -16,325 +17,332 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * &lt;p&gt;Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
  * 
- * &lt;p&gt;The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
- * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
- * &amp;lt;extension
- * base="{www.vamsas.ac.uk/jalview/version2}SequenceType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="DBRef" maxOccurs="unbounded"
- * minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&amp;gt;
- * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="source"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
- * name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;attribute name="accessionId"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
- * name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
- * /&amp;gt; &amp;lt;attribute name="canonical"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
- * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="dsseqid"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
- * name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;/extension&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
+ * <pre>
+ * &lt;complexType>
+ *   &lt;complexContent>
+ *     &lt;extension base="{www.vamsas.ac.uk/jalview/version2}SequenceType">
+ *       &lt;sequence>
+ *         &lt;element name="DBRef" maxOccurs="unbounded" minOccurs="0">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;sequence>
+ *                   &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
+ *                 &lt;/sequence>
+ *                 &lt;attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                 &lt;attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *       &lt;/sequence>
+ *       &lt;attribute name="dsseqid" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     &lt;/extension>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = { "dbRef" })
+@XmlType(name = "", propOrder = {
+    "dbRef"
+})
 @XmlRootElement(name = "Sequence")
-public class Sequence extends SequenceType
+public class Sequence
+    extends SequenceType
 {
 
-  @XmlElement(name = "DBRef")
-  protected List<Sequence.DBRef> dbRef;
-
-  @XmlAttribute(name = "dsseqid")
-  protected String dsseqid;
-
-  @XmlAttribute(name = "biotype")
-  protected String biotype;
-
-  /**
-   * Gets the value of the dbRef property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the dbRef property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getDBRef().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link Sequence.DBRef }
-   * 
-   * 
-   */
-  public List<Sequence.DBRef> getDBRef()
-  {
-    if (dbRef == null)
-    {
-      dbRef = new ArrayList<Sequence.DBRef>();
-    }
-    return this.dbRef;
-  }
-
-  /**
-   * Gets the value of the dsseqid property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDsseqid()
-  {
-    return dsseqid;
-  }
-
-  /**
-   * Sets the value of the dsseqid property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDsseqid(String value)
-  {
-    this.dsseqid = value;
-  }
-
-  /**
-   * Gets the value of the biotype property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getBiotype()
-  {
-    return biotype;
-  }
-
-  /**
-   * Sets the value of the biotype property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setBiotype(String value)
-  {
-    this.biotype = value;
-  }
-
-  /**
-   * &lt;p&gt;Java class for anonymous complex type.
-   * 
-   * &lt;p&gt;The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-   * &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
-   * &amp;lt;sequence&amp;gt; &amp;lt;element
-   * ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&amp;gt;
-   * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="source"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
-   * name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-   * &amp;lt;attribute name="accessionId"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
-   * name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean"
-   * default="false" /&amp;gt; &amp;lt;attribute name="canonical"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
-   * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "mapping" })
-  public static class DBRef
-  {
-
-    @XmlElement(name = "Mapping")
-    protected Mapping mapping;
-
-    @XmlAttribute(name = "source")
-    protected String source;
-
-    @XmlAttribute(name = "version")
-    protected String version;
-
-    @XmlAttribute(name = "accessionId")
-    protected String accessionId;
-
-    @XmlAttribute(name = "locus")
-    protected Boolean locus;
-
-    @XmlAttribute(name = "canonical")
-    protected Boolean canonical;
+    @XmlElement(name = "DBRef")
+    protected List<Sequence.DBRef> dbRef;
+    @XmlAttribute(name = "dsseqid")
+    protected String dsseqid;
+    @XmlAttribute(name = "biotype")
+    protected String biotype;
 
     /**
-     * Gets the value of the mapping property.
+     * Gets the value of the dbRef property.
      * 
-     * @return possible object is {@link Mapping }
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the dbRef property.
      * 
-     */
-    public Mapping getMapping()
-    {
-      return mapping;
-    }
-
-    /**
-     * Sets the value of the mapping property.
-     * 
-     * @param value
-     *          allowed object is {@link Mapping }
-     * 
-     */
-    public void setMapping(Mapping value)
-    {
-      this.mapping = value;
-    }
-
-    /**
-     * Gets the value of the source property.
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getDBRef().add(newItem);
+     * </pre>
      * 
-     * @return possible object is {@link String }
      * 
-     */
-    public String getSource()
-    {
-      return source;
-    }
-
-    /**
-     * Sets the value of the source property.
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link Sequence.DBRef }
      * 
-     * @param value
-     *          allowed object is {@link String }
      * 
      */
-    public void setSource(String value)
-    {
-      this.source = value;
+    public List<Sequence.DBRef> getDBRef() {
+        if (dbRef == null) {
+            dbRef = new ArrayList<Sequence.DBRef>();
+        }
+        return this.dbRef;
     }
 
     /**
-     * Gets the value of the version property.
-     * 
-     * @return possible object is {@link String }
+     * Gets the value of the dsseqid property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getVersion()
-    {
-      return version;
+    public String getDsseqid() {
+        return dsseqid;
     }
 
     /**
-     * Sets the value of the version property.
+     * Sets the value of the dsseqid property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setVersion(String value)
-    {
-      this.version = value;
+    public void setDsseqid(String value) {
+        this.dsseqid = value;
     }
 
     /**
-     * Gets the value of the accessionId property.
-     * 
-     * @return possible object is {@link String }
+     * Gets the value of the biotype property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getAccessionId()
-    {
-      return accessionId;
+    public String getBiotype() {
+        return biotype;
     }
 
     /**
-     * Sets the value of the accessionId property.
+     * Sets the value of the biotype property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setAccessionId(String value)
-    {
-      this.accessionId = value;
+    public void setBiotype(String value) {
+        this.biotype = value;
     }
 
-    /**
-     * Gets the value of the locus property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isLocus()
-    {
-      if (locus == null)
-      {
-        return false;
-      }
-      else
-      {
-        return locus;
-      }
-    }
 
     /**
-     * Sets the value of the locus property.
+     * <p>Java class for anonymous complex type.
      * 
-     * @param value
-     *          allowed object is {@link Boolean }
+     * <p>The following schema fragment specifies the expected content contained within this class.
      * 
-     */
-    public void setLocus(Boolean value)
-    {
-      this.locus = value;
-    }
-
-    /**
-     * Gets the value of the canonical property.
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
+     *       &lt;/sequence>
+     *       &lt;attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
      * 
-     * @return possible object is {@link Boolean }
      * 
      */
-    public boolean isCanonical()
-    {
-      if (canonical == null)
-      {
-        return false;
-      }
-      else
-      {
-        return canonical;
-      }
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "mapping"
+    })
+    public static class DBRef {
+
+        @XmlElement(name = "Mapping")
+        protected Mapping mapping;
+        @XmlAttribute(name = "source")
+        protected String source;
+        @XmlAttribute(name = "version")
+        protected String version;
+        @XmlAttribute(name = "accessionId")
+        protected String accessionId;
+        @XmlAttribute(name = "locus")
+        protected Boolean locus;
+        @XmlAttribute(name = "canonical")
+        protected Boolean canonical;
+
+        /**
+         * Gets the value of the mapping property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Mapping }
+         *     
+         */
+        public Mapping getMapping() {
+            return mapping;
+        }
+
+        /**
+         * Sets the value of the mapping property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Mapping }
+         *     
+         */
+        public void setMapping(Mapping value) {
+            this.mapping = value;
+        }
+
+        /**
+         * Gets the value of the source property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getSource() {
+            return source;
+        }
+
+        /**
+         * Sets the value of the source property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setSource(String value) {
+            this.source = value;
+        }
+
+        /**
+         * Gets the value of the version property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getVersion() {
+            return version;
+        }
+
+        /**
+         * Sets the value of the version property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setVersion(String value) {
+            this.version = value;
+        }
+
+        /**
+         * Gets the value of the accessionId property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getAccessionId() {
+            return accessionId;
+        }
+
+        /**
+         * Sets the value of the accessionId property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setAccessionId(String value) {
+            this.accessionId = value;
+        }
+
+        /**
+         * Gets the value of the locus property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isLocus() {
+            if (locus == null) {
+                return false;
+            } else {
+                return locus;
+            }
+        }
+
+        /**
+         * Sets the value of the locus property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setLocus(Boolean value) {
+            this.locus = value;
+        }
+
+        /**
+         * Gets the value of the canonical property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isCanonical() {
+            if (canonical == null) {
+                return false;
+            } else {
+                return canonical;
+            }
+        }
+
+        /**
+         * Sets the value of the canonical property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setCanonical(Boolean value) {
+            this.canonical = value;
+        }
 
-    /**
-     * Sets the value of the canonical property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setCanonical(Boolean value)
-    {
-      this.canonical = value;
     }
 
-  }
-
 }
diff --git a/src/jalview/xml/binding/jalview/SequenceSet.java b/src/jalview/xml/binding/jalview/SequenceSet.java
index d6464b3..ed2c120 100644
--- a/src/jalview/xml/binding/jalview/SequenceSet.java
+++ b/src/jalview/xml/binding/jalview/SequenceSet.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -16,287 +17,302 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * &lt;p&gt;Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
  * 
- * &lt;p&gt;The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
- * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
- * &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded"
- * minOccurs="0"/&amp;gt; &amp;lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded"
- * minOccurs="0"/&amp;gt; &amp;lt;element name="sequenceSetProperties"
- * maxOccurs="unbounded" minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
- * name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;attribute name="value"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded"
- * minOccurs="0"/&amp;gt; &amp;lt;/sequence&amp;gt; &amp;lt;attribute
- * name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&amp;gt; &amp;lt;attribute name="datasetId"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
+ * <pre>
+ * &lt;complexType>
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded" minOccurs="0"/>
+ *         &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded" minOccurs="0"/>
+ *         &lt;element name="sequenceSetProperties" maxOccurs="unbounded" minOccurs="0">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *         &lt;element ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" minOccurs="0"/>
+ *       &lt;/sequence>
+ *       &lt;attribute name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="datasetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "",
-  propOrder =
-  { "sequence", "annotation", "sequenceSetProperties", "alcodonFrame" })
+@XmlType(name = "", propOrder = {
+    "sequence",
+    "annotation",
+    "sequenceSetProperties",
+    "alcodonFrame"
+})
 @XmlRootElement(name = "SequenceSet")
-public class SequenceSet
-{
-
-  @XmlElement(name = "Sequence")
-  protected List<Sequence> sequence;
-
-  @XmlElement(name = "Annotation")
-  protected List<Annotation> annotation;
+public class SequenceSet {
 
-  protected List<SequenceSet.SequenceSetProperties> sequenceSetProperties;
+    @XmlElement(name = "Sequence")
+    protected List<Sequence> sequence;
+    @XmlElement(name = "Annotation")
+    protected List<Annotation> annotation;
+    protected List<SequenceSet.SequenceSetProperties> sequenceSetProperties;
+    @XmlElement(name = "AlcodonFrame")
+    protected List<AlcodonFrame> alcodonFrame;
+    @XmlAttribute(name = "gapChar", required = true)
+    protected String gapChar;
+    @XmlAttribute(name = "datasetId")
+    protected String datasetId;
 
-  @XmlElement(name = "AlcodonFrame")
-  protected List<AlcodonFrame> alcodonFrame;
-
-  @XmlAttribute(name = "gapChar", required = true)
-  protected String gapChar;
-
-  @XmlAttribute(name = "datasetId")
-  protected String datasetId;
-
-  /**
-   * Gets the value of the sequence property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the sequence property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getSequence().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link Sequence }
-   * 
-   * 
-   */
-  public List<Sequence> getSequence()
-  {
-    if (sequence == null)
-    {
-      sequence = new ArrayList<Sequence>();
+    /**
+     * Gets the value of the sequence property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the sequence property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getSequence().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link Sequence }
+     * 
+     * 
+     */
+    public List<Sequence> getSequence() {
+        if (sequence == null) {
+            sequence = new ArrayList<Sequence>();
+        }
+        return this.sequence;
     }
-    return this.sequence;
-  }
 
-  /**
-   * Gets the value of the annotation property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the annotation property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getAnnotation().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link Annotation }
-   * 
-   * 
-   */
-  public List<Annotation> getAnnotation()
-  {
-    if (annotation == null)
-    {
-      annotation = new ArrayList<Annotation>();
+    /**
+     * Gets the value of the annotation property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the annotation property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getAnnotation().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link Annotation }
+     * 
+     * 
+     */
+    public List<Annotation> getAnnotation() {
+        if (annotation == null) {
+            annotation = new ArrayList<Annotation>();
+        }
+        return this.annotation;
     }
-    return this.annotation;
-  }
 
-  /**
-   * Gets the value of the sequenceSetProperties property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the sequenceSetProperties property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getSequenceSetProperties().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link SequenceSet.SequenceSetProperties }
-   * 
-   * 
-   */
-  public List<SequenceSet.SequenceSetProperties> getSequenceSetProperties()
-  {
-    if (sequenceSetProperties == null)
-    {
-      sequenceSetProperties = new ArrayList<SequenceSet.SequenceSetProperties>();
+    /**
+     * Gets the value of the sequenceSetProperties property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the sequenceSetProperties property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getSequenceSetProperties().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link SequenceSet.SequenceSetProperties }
+     * 
+     * 
+     */
+    public List<SequenceSet.SequenceSetProperties> getSequenceSetProperties() {
+        if (sequenceSetProperties == null) {
+            sequenceSetProperties = new ArrayList<SequenceSet.SequenceSetProperties>();
+        }
+        return this.sequenceSetProperties;
     }
-    return this.sequenceSetProperties;
-  }
 
-  /**
-   * Gets the value of the alcodonFrame property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the alcodonFrame property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getAlcodonFrame().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link AlcodonFrame }
-   * 
-   * 
-   */
-  public List<AlcodonFrame> getAlcodonFrame()
-  {
-    if (alcodonFrame == null)
-    {
-      alcodonFrame = new ArrayList<AlcodonFrame>();
+    /**
+     * Gets the value of the alcodonFrame property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the alcodonFrame property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getAlcodonFrame().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link AlcodonFrame }
+     * 
+     * 
+     */
+    public List<AlcodonFrame> getAlcodonFrame() {
+        if (alcodonFrame == null) {
+            alcodonFrame = new ArrayList<AlcodonFrame>();
+        }
+        return this.alcodonFrame;
     }
-    return this.alcodonFrame;
-  }
-
-  /**
-   * Gets the value of the gapChar property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getGapChar()
-  {
-    return gapChar;
-  }
-
-  /**
-   * Sets the value of the gapChar property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setGapChar(String value)
-  {
-    this.gapChar = value;
-  }
-
-  /**
-   * Gets the value of the datasetId property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDatasetId()
-  {
-    return datasetId;
-  }
-
-  /**
-   * Sets the value of the datasetId property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDatasetId(String value)
-  {
-    this.datasetId = value;
-  }
-
-  /**
-   * &lt;p&gt;Java class for anonymous complex type.
-   * 
-   * &lt;p&gt;The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-   * &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
-   * name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-   * &amp;lt;attribute name="value"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-   * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class SequenceSetProperties
-  {
-
-    @XmlAttribute(name = "key")
-    protected String key;
-
-    @XmlAttribute(name = "value")
-    protected String value;
 
     /**
-     * Gets the value of the key property.
-     * 
-     * @return possible object is {@link String }
+     * Gets the value of the gapChar property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getKey()
-    {
-      return key;
+    public String getGapChar() {
+        return gapChar;
     }
 
     /**
-     * Sets the value of the key property.
+     * Sets the value of the gapChar property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setKey(String value)
-    {
-      this.key = value;
+    public void setGapChar(String value) {
+        this.gapChar = value;
     }
 
     /**
-     * Gets the value of the value property.
-     * 
-     * @return possible object is {@link String }
+     * Gets the value of the datasetId property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getValue()
-    {
-      return value;
+    public String getDatasetId() {
+        return datasetId;
     }
 
     /**
-     * Sets the value of the value property.
+     * Sets the value of the datasetId property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setValue(String value)
-    {
-      this.value = value;
+    public void setDatasetId(String value) {
+        this.datasetId = value;
     }
 
-  }
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class SequenceSetProperties {
+
+        @XmlAttribute(name = "key")
+        protected String key;
+        @XmlAttribute(name = "value")
+        protected String value;
+
+        /**
+         * Gets the value of the key property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getKey() {
+            return key;
+        }
+
+        /**
+         * Sets the value of the key property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setKey(String value) {
+            this.key = value;
+        }
+
+        /**
+         * Gets the value of the value property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getValue() {
+            return value;
+        }
+
+        /**
+         * Sets the value of the value property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setValue(String value) {
+            this.value = value;
+        }
+
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/SequenceType.java b/src/jalview/xml/binding/jalview/SequenceType.java
index 2e378da..cb7fa05 100644
--- a/src/jalview/xml/binding/jalview/SequenceType.java
+++ b/src/jalview/xml/binding/jalview/SequenceType.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,132 +14,140 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlSeeAlso;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * &lt;p&gt;Java class for SequenceType complex type.
+ * <p>Java class for SequenceType complex type.
  * 
- * &lt;p&gt;The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
- * &lt;pre&gt; &amp;lt;complexType name="SequenceType"&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="sequence"
- * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&amp;gt;
- * &amp;lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string"
- * minOccurs="0"/&amp;gt; &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="id"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
- * name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
+ * <pre>
+ * &lt;complexType name="SequenceType">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *       &lt;/sequence>
+ *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "SequenceType", propOrder = { "sequence", "name" })
-@XmlSeeAlso({ Sequence.class })
-public class SequenceType
-{
-
-  protected String sequence;
-
-  protected String name;
-
-  @XmlAttribute(name = "id")
-  protected String id;
-
-  @XmlAttribute(name = "description")
-  protected String description;
-
-  /**
-   * Gets the value of the sequence property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getSequence()
-  {
-    return sequence;
-  }
-
-  /**
-   * Sets the value of the sequence property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setSequence(String value)
-  {
-    this.sequence = value;
-  }
-
-  /**
-   * Gets the value of the name property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getName()
-  {
-    return name;
-  }
-
-  /**
-   * Sets the value of the name property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setName(String value)
-  {
-    this.name = value;
-  }
-
-  /**
-   * Gets the value of the id property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getId()
-  {
-    return id;
-  }
-
-  /**
-   * Sets the value of the id property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setId(String value)
-  {
-    this.id = value;
-  }
-
-  /**
-   * Gets the value of the description property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDescription()
-  {
-    return description;
-  }
-
-  /**
-   * Sets the value of the description property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDescription(String value)
-  {
-    this.description = value;
-  }
+@XmlType(name = "SequenceType", propOrder = {
+    "sequence",
+    "name"
+})
+@XmlSeeAlso({
+    Sequence.class
+})
+public class SequenceType {
+
+    protected String sequence;
+    protected String name;
+    @XmlAttribute(name = "id")
+    protected String id;
+    @XmlAttribute(name = "description")
+    protected String description;
+
+    /**
+     * Gets the value of the sequence property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getSequence() {
+        return sequence;
+    }
+
+    /**
+     * Sets the value of the sequence property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setSequence(String value) {
+        this.sequence = value;
+    }
+
+    /**
+     * Gets the value of the name property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getName() {
+        return name;
+    }
+
+    /**
+     * Sets the value of the name property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setName(String value) {
+        this.name = value;
+    }
+
+    /**
+     * Gets the value of the id property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getId() {
+        return id;
+    }
+
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setId(String value) {
+        this.id = value;
+    }
+
+    /**
+     * Gets the value of the description property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDescription() {
+        return description;
+    }
+
+    /**
+     * Sets the value of the description property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDescription(String value) {
+        this.description = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/ThresholdType.java b/src/jalview/xml/binding/jalview/ThresholdType.java
index 501c729..49c2dd2 100644
--- a/src/jalview/xml/binding/jalview/ThresholdType.java
+++ b/src/jalview/xml/binding/jalview/ThresholdType.java
@@ -1,42 +1,47 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlEnum;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * &lt;p&gt;Java class for ThresholdType.
+ * <p>Java class for ThresholdType.
  * 
- * &lt;p&gt;The following schema fragment specifies the expected content
- * contained within this class. &lt;pre&gt; &amp;lt;simpleType
- * name="ThresholdType"&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}string"&amp;gt; &amp;lt;enumeration
- * value="NONE"/&amp;gt; &amp;lt;enumeration value="ABOVE"/&amp;gt;
- * &amp;lt;enumeration value="BELOW"/&amp;gt; &amp;lt;/restriction&amp;gt;
- * &amp;lt;/simpleType&amp;gt; &lt;/pre&gt;
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * <pre>
+ * &lt;simpleType name="ThresholdType">
+ *   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ *     &lt;enumeration value="NONE"/>
+ *     &lt;enumeration value="ABOVE"/>
+ *     &lt;enumeration value="BELOW"/>
+ *   &lt;/restriction>
+ * &lt;/simpleType>
+ * </pre>
  * 
  */
 @XmlType(name = "ThresholdType", namespace = "www.jalview.org/colours")
 @XmlEnum
-public enum ThresholdType
-{
+public enum ThresholdType {
 
-  NONE, ABOVE, BELOW;
+    NONE,
+    ABOVE,
+    BELOW;
 
-  public String value()
-  {
-    return name();
-  }
+    public String value() {
+        return name();
+    }
 
-  public static ThresholdType fromValue(String v)
-  {
-    return valueOf(v);
-  }
+    public static ThresholdType fromValue(String v) {
+        return valueOf(v);
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/VAMSAS.java b/src/jalview/xml/binding/jalview/VAMSAS.java
index 932ba3b..d697534 100644
--- a/src/jalview/xml/binding/jalview/VAMSAS.java
+++ b/src/jalview/xml/binding/jalview/VAMSAS.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -14,85 +15,95 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * &lt;p&gt;Java class for VAMSAS complex type.
+ * <p>Java class for VAMSAS complex type.
  * 
- * &lt;p&gt;The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
- * &lt;pre&gt; &amp;lt;complexType name="VAMSAS"&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="Tree"
- * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"
- * minOccurs="0"/&amp;gt; &amp;lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}SequenceSet" maxOccurs="unbounded"
- * minOccurs="0"/&amp;gt; &amp;lt;/sequence&amp;gt; &amp;lt;/restriction&amp;gt;
- * &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
+ * <pre>
+ * &lt;complexType name="VAMSAS">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="Tree" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ *         &lt;element ref="{www.vamsas.ac.uk/jalview/version2}SequenceSet" maxOccurs="unbounded" minOccurs="0"/>
+ *       &lt;/sequence>
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "VAMSAS", propOrder = { "tree", "sequenceSet" })
-public class VAMSAS
-{
-
-  @XmlElement(name = "Tree")
-  protected List<String> tree;
+@XmlType(name = "VAMSAS", propOrder = {
+    "tree",
+    "sequenceSet"
+})
+public class VAMSAS {
 
-  @XmlElement(name = "SequenceSet")
-  protected List<SequenceSet> sequenceSet;
+    @XmlElement(name = "Tree")
+    protected List<String> tree;
+    @XmlElement(name = "SequenceSet")
+    protected List<SequenceSet> sequenceSet;
 
-  /**
-   * Gets the value of the tree property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the tree property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getTree().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link String }
-   * 
-   * 
-   */
-  public List<String> getTree()
-  {
-    if (tree == null)
-    {
-      tree = new ArrayList<String>();
+    /**
+     * Gets the value of the tree property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the tree property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getTree().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
+     * 
+     */
+    public List<String> getTree() {
+        if (tree == null) {
+            tree = new ArrayList<String>();
+        }
+        return this.tree;
     }
-    return this.tree;
-  }
 
-  /**
-   * Gets the value of the sequenceSet property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the sequenceSet property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getSequenceSet().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link SequenceSet }
-   * 
-   * 
-   */
-  public List<SequenceSet> getSequenceSet()
-  {
-    if (sequenceSet == null)
-    {
-      sequenceSet = new ArrayList<SequenceSet>();
+    /**
+     * Gets the value of the sequenceSet property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the sequenceSet property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getSequenceSet().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link SequenceSet }
+     * 
+     * 
+     */
+    public List<SequenceSet> getSequenceSet() {
+        if (sequenceSet == null) {
+            sequenceSet = new ArrayList<SequenceSet>();
+        }
+        return this.sequenceSet;
     }
-    return this.sequenceSet;
-  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
index 44d5829..1935391 100644
--- a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
+++ b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -17,173 +18,177 @@ import javax.xml.bind.annotation.XmlSchemaType;
 import javax.xml.bind.annotation.XmlSeeAlso;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * &lt;p&gt;Java class for WebServiceParameterSet complex type.
+ * <p>Java class for WebServiceParameterSet complex type.
  * 
- * &lt;p&gt;The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
- * &lt;pre&gt; &amp;lt;complexType name="WebServiceParameterSet"&amp;gt;
- * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
- * &amp;lt;sequence&amp;gt; &amp;lt;element name="Version"
- * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&amp;gt;
- * &amp;lt;element name="description"
- * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&amp;gt;
- * &amp;lt;element name="serviceURL"
- * type="{http://www.w3.org/2001/XMLSchema}anyURI"
- * maxOccurs="unbounded"/&amp;gt; &amp;lt;element name="parameters"
- * type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
- * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="name" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
- * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
- * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
+ * <pre>
+ * &lt;complexType name="WebServiceParameterSet">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         &lt;element name="serviceURL" type="{http://www.w3.org/2001/XMLSchema}anyURI" maxOccurs="unbounded"/>
+ *         &lt;element name="parameters" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *       &lt;/sequence>
+ *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "WebServiceParameterSet",
-  namespace = "www.jalview.org/xml/wsparamset",
-  propOrder =
-  { "version", "description", "serviceURL", "parameters" })
+@XmlType(name = "WebServiceParameterSet", namespace = "www.jalview.org/xml/wsparamset", propOrder = {
+    "version",
+    "description",
+    "serviceURL",
+    "parameters"
+})
 @XmlSeeAlso({
-    jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam.class })
-public class WebServiceParameterSet
-{
-
-  @XmlElement(name = "Version", namespace = "")
-  protected String version;
-
-  @XmlElement(namespace = "")
-  protected String description;
-
-  @XmlElement(namespace = "", required = true)
-  @XmlSchemaType(name = "anyURI")
-  protected List<String> serviceURL;
-
-  @XmlElement(namespace = "", required = true)
-  protected String parameters;
-
-  @XmlAttribute(name = "name", required = true)
-  protected String name;
-
-  /**
-   * Gets the value of the version property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getVersion()
-  {
-    return version;
-  }
-
-  /**
-   * Sets the value of the version property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setVersion(String value)
-  {
-    this.version = value;
-  }
-
-  /**
-   * Gets the value of the description property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDescription()
-  {
-    return description;
-  }
-
-  /**
-   * Sets the value of the description property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDescription(String value)
-  {
-    this.description = value;
-  }
-
-  /**
-   * Gets the value of the serviceURL property.
-   * 
-   * &lt;p&gt; This accessor method returns a reference to the live list, not a
-   * snapshot. Therefore any modification you make to the returned list will be
-   * present inside the JAXB object. This is why there is not a
-   * &lt;CODE&gt;set&lt;/CODE&gt; method for the serviceURL property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getServiceURL().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link String }
-   * 
-   * 
-   */
-  public List<String> getServiceURL()
-  {
-    if (serviceURL == null)
-    {
-      serviceURL = new ArrayList<String>();
+    jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam.class
+})
+public class WebServiceParameterSet {
+
+    @XmlElement(name = "Version", namespace = "")
+    protected String version;
+    @XmlElement(namespace = "")
+    protected String description;
+    @XmlElement(namespace = "", required = true)
+    @XmlSchemaType(name = "anyURI")
+    protected List<String> serviceURL;
+    @XmlElement(namespace = "", required = true)
+    protected String parameters;
+    @XmlAttribute(name = "name", required = true)
+    protected String name;
+
+    /**
+     * Gets the value of the version property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getVersion() {
+        return version;
+    }
+
+    /**
+     * Sets the value of the version property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setVersion(String value) {
+        this.version = value;
+    }
+
+    /**
+     * Gets the value of the description property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDescription() {
+        return description;
+    }
+
+    /**
+     * Sets the value of the description property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDescription(String value) {
+        this.description = value;
+    }
+
+    /**
+     * Gets the value of the serviceURL property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the serviceURL property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getServiceURL().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
+     * 
+     */
+    public List<String> getServiceURL() {
+        if (serviceURL == null) {
+            serviceURL = new ArrayList<String>();
+        }
+        return this.serviceURL;
+    }
+
+    /**
+     * Gets the value of the parameters property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getParameters() {
+        return parameters;
+    }
+
+    /**
+     * Sets the value of the parameters property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setParameters(String value) {
+        this.parameters = value;
+    }
+
+    /**
+     * Gets the value of the name property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getName() {
+        return name;
+    }
+
+    /**
+     * Sets the value of the name property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setName(String value) {
+        this.name = value;
     }
-    return this.serviceURL;
-  }
-
-  /**
-   * Gets the value of the parameters property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getParameters()
-  {
-    return parameters;
-  }
-
-  /**
-   * Sets the value of the parameters property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setParameters(String value)
-  {
-    this.parameters = value;
-  }
-
-  /**
-   * Gets the value of the name property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getName()
-  {
-    return name;
-  }
-
-  /**
-   * Sets the value of the name property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setName(String value)
-  {
-    this.name = value;
-  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/package-info.java b/src/jalview/xml/binding/jalview/package-info.java
index aa2ab9e..338e645 100644
--- a/src/jalview/xml/binding/jalview/package-info.java
+++ b/src/jalview/xml/binding/jalview/package-info.java
@@ -1,11 +1,9 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
-@javax.xml.bind.annotation.XmlSchema(
-  namespace = "www.vamsas.ac.uk/jalview/version2",
-  elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
+@javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
 package jalview.xml.binding.jalview;
diff --git a/src/jalview/xml/binding/uniprot/CitationType.java b/src/jalview/xml/binding/uniprot/CitationType.java
index b38df87..b07b8e2 100644
--- a/src/jalview/xml/binding/uniprot/CitationType.java
+++ b/src/jalview/xml/binding/uniprot/CitationType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -14,16 +15,14 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes different types of citations. Equivalent to the flat file RX-, RG-,
- * RA-, RT- and RL-lines.
+ * Describes different types of citations.
+ *             Equivalent to the flat file RX-, RG-, RA-, RT- and RL-lines.
  * 
- * <p>
- * Java class for citationType complex type.
+ * <p>Java class for citationType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="citationType">
@@ -73,457 +72,456 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "citationType",
-  propOrder =
-  { "title", "editorList", "authorList", "locator", "dbReference" })
-public class CitationType
-{
-
-  protected String title;
-
-  protected NameListType editorList;
-
-  protected NameListType authorList;
-
-  protected String locator;
-
-  protected List<DbReferenceType> dbReference;
-
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
-
-  @XmlAttribute(name = "date")
-  protected String date;
-
-  @XmlAttribute(name = "name")
-  protected String name;
-
-  @XmlAttribute(name = "volume")
-  protected String volume;
-
-  @XmlAttribute(name = "first")
-  protected String first;
-
-  @XmlAttribute(name = "last")
-  protected String last;
-
-  @XmlAttribute(name = "publisher")
-  protected String publisher;
-
-  @XmlAttribute(name = "city")
-  protected String city;
-
-  @XmlAttribute(name = "db")
-  protected String db;
-
-  @XmlAttribute(name = "number")
-  protected String number;
-
-  @XmlAttribute(name = "institute")
-  protected String institute;
-
-  @XmlAttribute(name = "country")
-  protected String country;
-
-  /**
-   * Gets the value of the title property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getTitle()
-  {
-    return title;
-  }
-
-  /**
-   * Sets the value of the title property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setTitle(String value)
-  {
-    this.title = value;
-  }
-
-  /**
-   * Gets the value of the editorList property.
-   * 
-   * @return possible object is {@link NameListType }
-   * 
-   */
-  public NameListType getEditorList()
-  {
-    return editorList;
-  }
-
-  /**
-   * Sets the value of the editorList property.
-   * 
-   * @param value
-   *          allowed object is {@link NameListType }
-   * 
-   */
-  public void setEditorList(NameListType value)
-  {
-    this.editorList = value;
-  }
-
-  /**
-   * Gets the value of the authorList property.
-   * 
-   * @return possible object is {@link NameListType }
-   * 
-   */
-  public NameListType getAuthorList()
-  {
-    return authorList;
-  }
-
-  /**
-   * Sets the value of the authorList property.
-   * 
-   * @param value
-   *          allowed object is {@link NameListType }
-   * 
-   */
-  public void setAuthorList(NameListType value)
-  {
-    this.authorList = value;
-  }
-
-  /**
-   * Gets the value of the locator property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getLocator()
-  {
-    return locator;
-  }
-
-  /**
-   * Sets the value of the locator property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setLocator(String value)
-  {
-    this.locator = value;
-  }
-
-  /**
-   * Gets the value of the dbReference property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the dbReference property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getDbReference().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link DbReferenceType }
-   * 
-   * 
-   */
-  public List<DbReferenceType> getDbReference()
-  {
-    if (dbReference == null)
-    {
-      dbReference = new ArrayList<DbReferenceType>();
-    }
-    return this.dbReference;
-  }
-
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
-
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
-
-  /**
-   * Gets the value of the date property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDate()
-  {
-    return date;
-  }
-
-  /**
-   * Sets the value of the date property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDate(String value)
-  {
-    this.date = value;
-  }
-
-  /**
-   * Gets the value of the name property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getName()
-  {
-    return name;
-  }
-
-  /**
-   * Sets the value of the name property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setName(String value)
-  {
-    this.name = value;
-  }
-
-  /**
-   * Gets the value of the volume property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getVolume()
-  {
-    return volume;
-  }
-
-  /**
-   * Sets the value of the volume property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setVolume(String value)
-  {
-    this.volume = value;
-  }
-
-  /**
-   * Gets the value of the first property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getFirst()
-  {
-    return first;
-  }
-
-  /**
-   * Sets the value of the first property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setFirst(String value)
-  {
-    this.first = value;
-  }
-
-  /**
-   * Gets the value of the last property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getLast()
-  {
-    return last;
-  }
-
-  /**
-   * Sets the value of the last property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setLast(String value)
-  {
-    this.last = value;
-  }
-
-  /**
-   * Gets the value of the publisher property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getPublisher()
-  {
-    return publisher;
-  }
-
-  /**
-   * Sets the value of the publisher property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setPublisher(String value)
-  {
-    this.publisher = value;
-  }
-
-  /**
-   * Gets the value of the city property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getCity()
-  {
-    return city;
-  }
-
-  /**
-   * Sets the value of the city property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setCity(String value)
-  {
-    this.city = value;
-  }
-
-  /**
-   * Gets the value of the db property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDb()
-  {
-    return db;
-  }
-
-  /**
-   * Sets the value of the db property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDb(String value)
-  {
-    this.db = value;
-  }
-
-  /**
-   * Gets the value of the number property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getNumber()
-  {
-    return number;
-  }
-
-  /**
-   * Sets the value of the number property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setNumber(String value)
-  {
-    this.number = value;
-  }
-
-  /**
-   * Gets the value of the institute property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getInstitute()
-  {
-    return institute;
-  }
-
-  /**
-   * Sets the value of the institute property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setInstitute(String value)
-  {
-    this.institute = value;
-  }
-
-  /**
-   * Gets the value of the country property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getCountry()
-  {
-    return country;
-  }
-
-  /**
-   * Sets the value of the country property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setCountry(String value)
-  {
-    this.country = value;
-  }
+@XmlType(name = "citationType", propOrder = {
+    "title",
+    "editorList",
+    "authorList",
+    "locator",
+    "dbReference"
+})
+public class CitationType {
+
+    protected String title;
+    protected NameListType editorList;
+    protected NameListType authorList;
+    protected String locator;
+    protected List<DbReferenceType> dbReference;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
+    @XmlAttribute(name = "date")
+    protected String date;
+    @XmlAttribute(name = "name")
+    protected String name;
+    @XmlAttribute(name = "volume")
+    protected String volume;
+    @XmlAttribute(name = "first")
+    protected String first;
+    @XmlAttribute(name = "last")
+    protected String last;
+    @XmlAttribute(name = "publisher")
+    protected String publisher;
+    @XmlAttribute(name = "city")
+    protected String city;
+    @XmlAttribute(name = "db")
+    protected String db;
+    @XmlAttribute(name = "number")
+    protected String number;
+    @XmlAttribute(name = "institute")
+    protected String institute;
+    @XmlAttribute(name = "country")
+    protected String country;
+
+    /**
+     * Gets the value of the title property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getTitle() {
+        return title;
+    }
+
+    /**
+     * Sets the value of the title property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setTitle(String value) {
+        this.title = value;
+    }
+
+    /**
+     * Gets the value of the editorList property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link NameListType }
+     *     
+     */
+    public NameListType getEditorList() {
+        return editorList;
+    }
+
+    /**
+     * Sets the value of the editorList property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link NameListType }
+     *     
+     */
+    public void setEditorList(NameListType value) {
+        this.editorList = value;
+    }
+
+    /**
+     * Gets the value of the authorList property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link NameListType }
+     *     
+     */
+    public NameListType getAuthorList() {
+        return authorList;
+    }
+
+    /**
+     * Sets the value of the authorList property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link NameListType }
+     *     
+     */
+    public void setAuthorList(NameListType value) {
+        this.authorList = value;
+    }
+
+    /**
+     * Gets the value of the locator property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getLocator() {
+        return locator;
+    }
+
+    /**
+     * Sets the value of the locator property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setLocator(String value) {
+        this.locator = value;
+    }
+
+    /**
+     * Gets the value of the dbReference property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the dbReference property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getDbReference().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link DbReferenceType }
+     * 
+     * 
+     */
+    public List<DbReferenceType> getDbReference() {
+        if (dbReference == null) {
+            dbReference = new ArrayList<DbReferenceType>();
+        }
+        return this.dbReference;
+    }
+
+    /**
+     * Gets the value of the type property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getType() {
+        return type;
+    }
+
+    /**
+     * Sets the value of the type property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
+
+    /**
+     * Gets the value of the date property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDate() {
+        return date;
+    }
+
+    /**
+     * Sets the value of the date property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDate(String value) {
+        this.date = value;
+    }
+
+    /**
+     * Gets the value of the name property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getName() {
+        return name;
+    }
+
+    /**
+     * Sets the value of the name property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setName(String value) {
+        this.name = value;
+    }
+
+    /**
+     * Gets the value of the volume property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getVolume() {
+        return volume;
+    }
+
+    /**
+     * Sets the value of the volume property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setVolume(String value) {
+        this.volume = value;
+    }
+
+    /**
+     * Gets the value of the first property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getFirst() {
+        return first;
+    }
+
+    /**
+     * Sets the value of the first property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setFirst(String value) {
+        this.first = value;
+    }
+
+    /**
+     * Gets the value of the last property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getLast() {
+        return last;
+    }
+
+    /**
+     * Sets the value of the last property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setLast(String value) {
+        this.last = value;
+    }
+
+    /**
+     * Gets the value of the publisher property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getPublisher() {
+        return publisher;
+    }
+
+    /**
+     * Sets the value of the publisher property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setPublisher(String value) {
+        this.publisher = value;
+    }
+
+    /**
+     * Gets the value of the city property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getCity() {
+        return city;
+    }
+
+    /**
+     * Sets the value of the city property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setCity(String value) {
+        this.city = value;
+    }
+
+    /**
+     * Gets the value of the db property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDb() {
+        return db;
+    }
+
+    /**
+     * Sets the value of the db property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDb(String value) {
+        this.db = value;
+    }
+
+    /**
+     * Gets the value of the number property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getNumber() {
+        return number;
+    }
+
+    /**
+     * Sets the value of the number property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setNumber(String value) {
+        this.number = value;
+    }
+
+    /**
+     * Gets the value of the institute property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getInstitute() {
+        return institute;
+    }
+
+    /**
+     * Sets the value of the institute property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setInstitute(String value) {
+        this.institute = value;
+    }
+
+    /**
+     * Gets the value of the country property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getCountry() {
+        return country;
+    }
+
+    /**
+     * Sets the value of the country property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setCountry(String value) {
+        this.country = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/CofactorType.java b/src/jalview/xml/binding/uniprot/CofactorType.java
index 424bcff..7dc9df3 100644
--- a/src/jalview/xml/binding/uniprot/CofactorType.java
+++ b/src/jalview/xml/binding/uniprot/CofactorType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,15 +16,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
  * Describes a cofactor.
  * 
- * <p>
- * Java class for cofactorType complex type.
+ * <p>Java class for cofactorType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="cofactorType">
@@ -42,94 +41,94 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "cofactorType", propOrder = { "name", "dbReference" })
-public class CofactorType
-{
-
-  @XmlElement(required = true)
-  protected String name;
-
-  @XmlElement(required = true)
-  protected DbReferenceType dbReference;
+@XmlType(name = "cofactorType", propOrder = {
+    "name",
+    "dbReference"
+})
+public class CofactorType {
 
-  @XmlAttribute(name = "evidence")
-  protected List<Integer> evidence;
+    @XmlElement(required = true)
+    protected String name;
+    @XmlElement(required = true)
+    protected DbReferenceType dbReference;
+    @XmlAttribute(name = "evidence")
+    protected List<Integer> evidence;
 
-  /**
-   * Gets the value of the name property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getName()
-  {
-    return name;
-  }
+    /**
+     * Gets the value of the name property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getName() {
+        return name;
+    }
 
-  /**
-   * Sets the value of the name property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setName(String value)
-  {
-    this.name = value;
-  }
+    /**
+     * Sets the value of the name property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setName(String value) {
+        this.name = value;
+    }
 
-  /**
-   * Gets the value of the dbReference property.
-   * 
-   * @return possible object is {@link DbReferenceType }
-   * 
-   */
-  public DbReferenceType getDbReference()
-  {
-    return dbReference;
-  }
+    /**
+     * Gets the value of the dbReference property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link DbReferenceType }
+     *     
+     */
+    public DbReferenceType getDbReference() {
+        return dbReference;
+    }
 
-  /**
-   * Sets the value of the dbReference property.
-   * 
-   * @param value
-   *          allowed object is {@link DbReferenceType }
-   * 
-   */
-  public void setDbReference(DbReferenceType value)
-  {
-    this.dbReference = value;
-  }
+    /**
+     * Sets the value of the dbReference property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link DbReferenceType }
+     *     
+     */
+    public void setDbReference(DbReferenceType value) {
+        this.dbReference = value;
+    }
 
-  /**
-   * Gets the value of the evidence property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the evidence property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getEvidence().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List<Integer> getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList<Integer>();
+    /**
+     * Gets the value of the evidence property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the evidence property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getEvidence().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link Integer }
+     * 
+     * 
+     */
+    public List<Integer> getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList<Integer>();
+        }
+        return this.evidence;
     }
-    return this.evidence;
-  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/CommentType.java b/src/jalview/xml/binding/uniprot/CommentType.java
index afd1da1..8766f7a 100644
--- a/src/jalview/xml/binding/uniprot/CommentType.java
+++ b/src/jalview/xml/binding/uniprot/CommentType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -16,16 +17,14 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlSchemaType;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes different types of general annotations. Equivalent to the flat file
- * CC-line.
+ * Describes different types of general annotations.
+ *             Equivalent to the flat file CC-line.
  * 
- * <p>
- * Java class for commentType complex type.
+ * <p>Java class for commentType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="commentType">
@@ -174,1673 +173,1619 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "commentType",
-  propOrder =
-  { "molecule", "absorption", "kinetics", "phDependence", "redoxPotential",
-      "temperatureDependence", "reaction", "physiologicalReaction",
-      "cofactor", "subcellularLocation", "conflict", "link", "event",
-      "isoform", "interactant", "organismsDiffer", "experiments", "disease",
-      "location", "text" })
-public class CommentType
-{
-
-  protected MoleculeType molecule;
-
-  protected CommentType.Absorption absorption;
-
-  protected CommentType.Kinetics kinetics;
-
-  protected CommentType.PhDependence phDependence;
-
-  protected CommentType.RedoxPotential redoxPotential;
-
-  protected CommentType.TemperatureDependence temperatureDependence;
-
-  protected ReactionType reaction;
-
-  protected List<PhysiologicalReactionType> physiologicalReaction;
-
-  protected List<CofactorType> cofactor;
-
-  protected List<SubcellularLocationType> subcellularLocation;
-
-  protected CommentType.Conflict conflict;
-
-  protected List<CommentType.Link> link;
+@XmlType(name = "commentType", propOrder = {
+    "molecule",
+    "absorption",
+    "kinetics",
+    "phDependence",
+    "redoxPotential",
+    "temperatureDependence",
+    "reaction",
+    "physiologicalReaction",
+    "cofactor",
+    "subcellularLocation",
+    "conflict",
+    "link",
+    "event",
+    "isoform",
+    "interactant",
+    "organismsDiffer",
+    "experiments",
+    "disease",
+    "location",
+    "text"
+})
+public class CommentType {
+
+    protected MoleculeType molecule;
+    protected CommentType.Absorption absorption;
+    protected CommentType.Kinetics kinetics;
+    protected CommentType.PhDependence phDependence;
+    protected CommentType.RedoxPotential redoxPotential;
+    protected CommentType.TemperatureDependence temperatureDependence;
+    protected ReactionType reaction;
+    protected List<PhysiologicalReactionType> physiologicalReaction;
+    protected List<CofactorType> cofactor;
+    protected List<SubcellularLocationType> subcellularLocation;
+    protected CommentType.Conflict conflict;
+    protected List<CommentType.Link> link;
+    protected List<EventType> event;
+    protected List<IsoformType> isoform;
+    protected List<InteractantType> interactant;
+    @XmlElement(defaultValue = "false")
+    protected Boolean organismsDiffer;
+    protected Integer experiments;
+    protected CommentType.Disease disease;
+    protected List<LocationType> location;
+    protected List<EvidencedStringType> text;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
+    @XmlAttribute(name = "locationType")
+    protected String locationType;
+    @XmlAttribute(name = "name")
+    protected String name;
+    @XmlAttribute(name = "mass")
+    protected Float mass;
+    @XmlAttribute(name = "error")
+    protected String error;
+    @XmlAttribute(name = "method")
+    protected String method;
+    @XmlAttribute(name = "evidence")
+    protected List<Integer> evidence;
 
-  protected List<EventType> event;
-
-  protected List<IsoformType> isoform;
-
-  protected List<InteractantType> interactant;
-
-  @XmlElement(defaultValue = "false")
-  protected Boolean organismsDiffer;
-
-  protected Integer experiments;
-
-  protected CommentType.Disease disease;
-
-  protected List<LocationType> location;
-
-  protected List<EvidencedStringType> text;
-
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
-
-  @XmlAttribute(name = "locationType")
-  protected String locationType;
-
-  @XmlAttribute(name = "name")
-  protected String name;
-
-  @XmlAttribute(name = "mass")
-  protected Float mass;
-
-  @XmlAttribute(name = "error")
-  protected String error;
-
-  @XmlAttribute(name = "method")
-  protected String method;
-
-  @XmlAttribute(name = "evidence")
-  protected List<Integer> evidence;
-
-  /**
-   * Gets the value of the molecule property.
-   * 
-   * @return possible object is {@link MoleculeType }
-   * 
-   */
-  public MoleculeType getMolecule()
-  {
-    return molecule;
-  }
-
-  /**
-   * Sets the value of the molecule property.
-   * 
-   * @param value
-   *          allowed object is {@link MoleculeType }
-   * 
-   */
-  public void setMolecule(MoleculeType value)
-  {
-    this.molecule = value;
-  }
-
-  /**
-   * Gets the value of the absorption property.
-   * 
-   * @return possible object is {@link CommentType.Absorption }
-   * 
-   */
-  public CommentType.Absorption getAbsorption()
-  {
-    return absorption;
-  }
-
-  /**
-   * Sets the value of the absorption property.
-   * 
-   * @param value
-   *          allowed object is {@link CommentType.Absorption }
-   * 
-   */
-  public void setAbsorption(CommentType.Absorption value)
-  {
-    this.absorption = value;
-  }
-
-  /**
-   * Gets the value of the kinetics property.
-   * 
-   * @return possible object is {@link CommentType.Kinetics }
-   * 
-   */
-  public CommentType.Kinetics getKinetics()
-  {
-    return kinetics;
-  }
-
-  /**
-   * Sets the value of the kinetics property.
-   * 
-   * @param value
-   *          allowed object is {@link CommentType.Kinetics }
-   * 
-   */
-  public void setKinetics(CommentType.Kinetics value)
-  {
-    this.kinetics = value;
-  }
-
-  /**
-   * Gets the value of the phDependence property.
-   * 
-   * @return possible object is {@link CommentType.PhDependence }
-   * 
-   */
-  public CommentType.PhDependence getPhDependence()
-  {
-    return phDependence;
-  }
-
-  /**
-   * Sets the value of the phDependence property.
-   * 
-   * @param value
-   *          allowed object is {@link CommentType.PhDependence }
-   * 
-   */
-  public void setPhDependence(CommentType.PhDependence value)
-  {
-    this.phDependence = value;
-  }
-
-  /**
-   * Gets the value of the redoxPotential property.
-   * 
-   * @return possible object is {@link CommentType.RedoxPotential }
-   * 
-   */
-  public CommentType.RedoxPotential getRedoxPotential()
-  {
-    return redoxPotential;
-  }
-
-  /**
-   * Sets the value of the redoxPotential property.
-   * 
-   * @param value
-   *          allowed object is {@link CommentType.RedoxPotential }
-   * 
-   */
-  public void setRedoxPotential(CommentType.RedoxPotential value)
-  {
-    this.redoxPotential = value;
-  }
-
-  /**
-   * Gets the value of the temperatureDependence property.
-   * 
-   * @return possible object is {@link CommentType.TemperatureDependence }
-   * 
-   */
-  public CommentType.TemperatureDependence getTemperatureDependence()
-  {
-    return temperatureDependence;
-  }
-
-  /**
-   * Sets the value of the temperatureDependence property.
-   * 
-   * @param value
-   *          allowed object is {@link CommentType.TemperatureDependence }
-   * 
-   */
-  public void setTemperatureDependence(
-          CommentType.TemperatureDependence value)
-  {
-    this.temperatureDependence = value;
-  }
-
-  /**
-   * Gets the value of the reaction property.
-   * 
-   * @return possible object is {@link ReactionType }
-   * 
-   */
-  public ReactionType getReaction()
-  {
-    return reaction;
-  }
-
-  /**
-   * Sets the value of the reaction property.
-   * 
-   * @param value
-   *          allowed object is {@link ReactionType }
-   * 
-   */
-  public void setReaction(ReactionType value)
-  {
-    this.reaction = value;
-  }
-
-  /**
-   * Gets the value of the physiologicalReaction property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the physiologicalReaction property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getPhysiologicalReaction().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link PhysiologicalReactionType }
-   * 
-   * 
-   */
-  public List<PhysiologicalReactionType> getPhysiologicalReaction()
-  {
-    if (physiologicalReaction == null)
-    {
-      physiologicalReaction = new ArrayList<PhysiologicalReactionType>();
+    /**
+     * Gets the value of the molecule property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link MoleculeType }
+     *     
+     */
+    public MoleculeType getMolecule() {
+        return molecule;
     }
-    return this.physiologicalReaction;
-  }
-
-  /**
-   * Gets the value of the cofactor property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the cofactor property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getCofactor().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link CofactorType }
-   * 
-   * 
-   */
-  public List<CofactorType> getCofactor()
-  {
-    if (cofactor == null)
-    {
-      cofactor = new ArrayList<CofactorType>();
+
+    /**
+     * Sets the value of the molecule property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link MoleculeType }
+     *     
+     */
+    public void setMolecule(MoleculeType value) {
+        this.molecule = value;
     }
-    return this.cofactor;
-  }
-
-  /**
-   * Gets the value of the subcellularLocation property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the subcellularLocation property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getSubcellularLocation().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link SubcellularLocationType }
-   * 
-   * 
-   */
-  public List<SubcellularLocationType> getSubcellularLocation()
-  {
-    if (subcellularLocation == null)
-    {
-      subcellularLocation = new ArrayList<SubcellularLocationType>();
+
+    /**
+     * Gets the value of the absorption property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link CommentType.Absorption }
+     *     
+     */
+    public CommentType.Absorption getAbsorption() {
+        return absorption;
     }
-    return this.subcellularLocation;
-  }
-
-  /**
-   * Gets the value of the conflict property.
-   * 
-   * @return possible object is {@link CommentType.Conflict }
-   * 
-   */
-  public CommentType.Conflict getConflict()
-  {
-    return conflict;
-  }
-
-  /**
-   * Sets the value of the conflict property.
-   * 
-   * @param value
-   *          allowed object is {@link CommentType.Conflict }
-   * 
-   */
-  public void setConflict(CommentType.Conflict value)
-  {
-    this.conflict = value;
-  }
-
-  /**
-   * Gets the value of the link property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the link property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getLink().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link CommentType.Link }
-   * 
-   * 
-   */
-  public List<CommentType.Link> getLink()
-  {
-    if (link == null)
-    {
-      link = new ArrayList<CommentType.Link>();
+
+    /**
+     * Sets the value of the absorption property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link CommentType.Absorption }
+     *     
+     */
+    public void setAbsorption(CommentType.Absorption value) {
+        this.absorption = value;
     }
-    return this.link;
-  }
-
-  /**
-   * Gets the value of the event property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the event property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getEvent().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link EventType }
-   * 
-   * 
-   */
-  public List<EventType> getEvent()
-  {
-    if (event == null)
-    {
-      event = new ArrayList<EventType>();
+
+    /**
+     * Gets the value of the kinetics property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link CommentType.Kinetics }
+     *     
+     */
+    public CommentType.Kinetics getKinetics() {
+        return kinetics;
     }
-    return this.event;
-  }
-
-  /**
-   * Gets the value of the isoform property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the isoform property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getIsoform().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link IsoformType
-   * }
-   * 
-   * 
-   */
-  public List<IsoformType> getIsoform()
-  {
-    if (isoform == null)
-    {
-      isoform = new ArrayList<IsoformType>();
+
+    /**
+     * Sets the value of the kinetics property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link CommentType.Kinetics }
+     *     
+     */
+    public void setKinetics(CommentType.Kinetics value) {
+        this.kinetics = value;
     }
-    return this.isoform;
-  }
-
-  /**
-   * Gets the value of the interactant property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the interactant property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getInteractant().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link InteractantType }
-   * 
-   * 
-   */
-  public List<InteractantType> getInteractant()
-  {
-    if (interactant == null)
-    {
-      interactant = new ArrayList<InteractantType>();
+
+    /**
+     * Gets the value of the phDependence property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link CommentType.PhDependence }
+     *     
+     */
+    public CommentType.PhDependence getPhDependence() {
+        return phDependence;
     }
-    return this.interactant;
-  }
-
-  /**
-   * Gets the value of the organismsDiffer property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public Boolean isOrganismsDiffer()
-  {
-    return organismsDiffer;
-  }
-
-  /**
-   * Sets the value of the organismsDiffer property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setOrganismsDiffer(Boolean value)
-  {
-    this.organismsDiffer = value;
-  }
-
-  /**
-   * Gets the value of the experiments property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getExperiments()
-  {
-    return experiments;
-  }
-
-  /**
-   * Sets the value of the experiments property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setExperiments(Integer value)
-  {
-    this.experiments = value;
-  }
-
-  /**
-   * Gets the value of the disease property.
-   * 
-   * @return possible object is {@link CommentType.Disease }
-   * 
-   */
-  public CommentType.Disease getDisease()
-  {
-    return disease;
-  }
-
-  /**
-   * Sets the value of the disease property.
-   * 
-   * @param value
-   *          allowed object is {@link CommentType.Disease }
-   * 
-   */
-  public void setDisease(CommentType.Disease value)
-  {
-    this.disease = value;
-  }
-
-  /**
-   * Gets the value of the location property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the location property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getLocation().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link LocationType }
-   * 
-   * 
-   */
-  public List<LocationType> getLocation()
-  {
-    if (location == null)
-    {
-      location = new ArrayList<LocationType>();
+
+    /**
+     * Sets the value of the phDependence property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link CommentType.PhDependence }
+     *     
+     */
+    public void setPhDependence(CommentType.PhDependence value) {
+        this.phDependence = value;
     }
-    return this.location;
-  }
-
-  /**
-   * Gets the value of the text property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the text property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getText().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link EvidencedStringType }
-   * 
-   * 
-   */
-  public List<EvidencedStringType> getText()
-  {
-    if (text == null)
-    {
-      text = new ArrayList<EvidencedStringType>();
+
+    /**
+     * Gets the value of the redoxPotential property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link CommentType.RedoxPotential }
+     *     
+     */
+    public CommentType.RedoxPotential getRedoxPotential() {
+        return redoxPotential;
     }
-    return this.text;
-  }
-
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
-
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
-
-  /**
-   * Gets the value of the locationType property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getLocationType()
-  {
-    return locationType;
-  }
-
-  /**
-   * Sets the value of the locationType property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setLocationType(String value)
-  {
-    this.locationType = value;
-  }
-
-  /**
-   * Gets the value of the name property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getName()
-  {
-    return name;
-  }
-
-  /**
-   * Sets the value of the name property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setName(String value)
-  {
-    this.name = value;
-  }
-
-  /**
-   * Gets the value of the mass property.
-   * 
-   * @return possible object is {@link Float }
-   * 
-   */
-  public Float getMass()
-  {
-    return mass;
-  }
-
-  /**
-   * Sets the value of the mass property.
-   * 
-   * @param value
-   *          allowed object is {@link Float }
-   * 
-   */
-  public void setMass(Float value)
-  {
-    this.mass = value;
-  }
-
-  /**
-   * Gets the value of the error property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getError()
-  {
-    return error;
-  }
-
-  /**
-   * Sets the value of the error property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setError(String value)
-  {
-    this.error = value;
-  }
-
-  /**
-   * Gets the value of the method property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getMethod()
-  {
-    return method;
-  }
-
-  /**
-   * Sets the value of the method property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setMethod(String value)
-  {
-    this.method = value;
-  }
-
-  /**
-   * Gets the value of the evidence property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the evidence property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getEvidence().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List<Integer> getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList<Integer>();
+
+    /**
+     * Sets the value of the redoxPotential property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link CommentType.RedoxPotential }
+     *     
+     */
+    public void setRedoxPotential(CommentType.RedoxPotential value) {
+        this.redoxPotential = value;
     }
-    return this.evidence;
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;sequence>
-   *         &lt;element name="max" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
-   *         &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-   *       &lt;/sequence>
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "max", "text" })
-  public static class Absorption
-  {
-
-    protected EvidencedStringType max;
 
-    protected List<EvidencedStringType> text;
+    /**
+     * Gets the value of the temperatureDependence property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link CommentType.TemperatureDependence }
+     *     
+     */
+    public CommentType.TemperatureDependence getTemperatureDependence() {
+        return temperatureDependence;
+    }
 
     /**
-     * Gets the value of the max property.
+     * Sets the value of the temperatureDependence property.
      * 
-     * @return possible object is {@link EvidencedStringType }
+     * @param value
+     *     allowed object is
+     *     {@link CommentType.TemperatureDependence }
+     *     
+     */
+    public void setTemperatureDependence(CommentType.TemperatureDependence value) {
+        this.temperatureDependence = value;
+    }
+
+    /**
+     * Gets the value of the reaction property.
      * 
+     * @return
+     *     possible object is
+     *     {@link ReactionType }
+     *     
      */
-    public EvidencedStringType getMax()
-    {
-      return max;
+    public ReactionType getReaction() {
+        return reaction;
     }
 
     /**
-     * Sets the value of the max property.
+     * Sets the value of the reaction property.
      * 
      * @param value
-     *          allowed object is {@link EvidencedStringType }
-     * 
+     *     allowed object is
+     *     {@link ReactionType }
+     *     
      */
-    public void setMax(EvidencedStringType value)
-    {
-      this.max = value;
+    public void setReaction(ReactionType value) {
+        this.reaction = value;
     }
 
     /**
-     * Gets the value of the text property.
+     * Gets the value of the physiologicalReaction property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the text property.
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the physiologicalReaction property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
-     * 
      * <pre>
-     * getText().add(newItem);
+     *    getPhysiologicalReaction().add(newItem);
      * </pre>
      * 
      * 
      * <p>
      * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
+     * {@link PhysiologicalReactionType }
      * 
      * 
      */
-    public List<EvidencedStringType> getText()
-    {
-      if (text == null)
-      {
-        text = new ArrayList<EvidencedStringType>();
-      }
-      return this.text;
+    public List<PhysiologicalReactionType> getPhysiologicalReaction() {
+        if (physiologicalReaction == null) {
+            physiologicalReaction = new ArrayList<PhysiologicalReactionType>();
+        }
+        return this.physiologicalReaction;
     }
 
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;sequence>
-   *         &lt;element name="sequence" minOccurs="0">
-   *           &lt;complexType>
-   *             &lt;complexContent>
-   *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 &lt;attribute name="resource" use="required">
-   *                   &lt;simpleType>
-   *                     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
-   *                       &lt;enumeration value="EMBL-CDS"/>
-   *                       &lt;enumeration value="EMBL"/>
-   *                     &lt;/restriction>
-   *                   &lt;/simpleType>
-   *                 &lt;/attribute>
-   *                 &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *               &lt;/restriction>
-   *             &lt;/complexContent>
-   *           &lt;/complexType>
-   *         &lt;/element>
-   *       &lt;/sequence>
-   *       &lt;attribute name="type" use="required">
-   *         &lt;simpleType>
-   *           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
-   *             &lt;enumeration value="frameshift"/>
-   *             &lt;enumeration value="erroneous initiation"/>
-   *             &lt;enumeration value="erroneous termination"/>
-   *             &lt;enumeration value="erroneous gene model prediction"/>
-   *             &lt;enumeration value="erroneous translation"/>
-   *             &lt;enumeration value="miscellaneous discrepancy"/>
-   *           &lt;/restriction>
-   *         &lt;/simpleType>
-   *       &lt;/attribute>
-   *       &lt;attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "sequence" })
-  public static class Conflict
-  {
-
-    protected CommentType.Conflict.Sequence sequence;
-
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-
-    @XmlAttribute(name = "ref")
-    protected String ref;
-
     /**
-     * Gets the value of the sequence property.
+     * Gets the value of the cofactor property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the cofactor property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getCofactor().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link CofactorType }
      * 
-     * @return possible object is {@link CommentType.Conflict.Sequence }
      * 
      */
-    public CommentType.Conflict.Sequence getSequence()
-    {
-      return sequence;
+    public List<CofactorType> getCofactor() {
+        if (cofactor == null) {
+            cofactor = new ArrayList<CofactorType>();
+        }
+        return this.cofactor;
     }
 
     /**
-     * Sets the value of the sequence property.
+     * Gets the value of the subcellularLocation property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the subcellularLocation property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getSubcellularLocation().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link SubcellularLocationType }
      * 
-     * @param value
-     *          allowed object is {@link CommentType.Conflict.Sequence }
      * 
      */
-    public void setSequence(CommentType.Conflict.Sequence value)
-    {
-      this.sequence = value;
+    public List<SubcellularLocationType> getSubcellularLocation() {
+        if (subcellularLocation == null) {
+            subcellularLocation = new ArrayList<SubcellularLocationType>();
+        }
+        return this.subcellularLocation;
     }
 
     /**
-     * Gets the value of the type property.
-     * 
-     * @return possible object is {@link String }
+     * Gets the value of the conflict property.
      * 
+     * @return
+     *     possible object is
+     *     {@link CommentType.Conflict }
+     *     
      */
-    public String getType()
-    {
-      return type;
+    public CommentType.Conflict getConflict() {
+        return conflict;
     }
 
     /**
-     * Sets the value of the type property.
+     * Sets the value of the conflict property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link CommentType.Conflict }
+     *     
      */
-    public void setType(String value)
-    {
-      this.type = value;
+    public void setConflict(CommentType.Conflict value) {
+        this.conflict = value;
     }
 
     /**
-     * Gets the value of the ref property.
+     * Gets the value of the link property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the link property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getLink().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link CommentType.Link }
      * 
-     * @return possible object is {@link String }
      * 
      */
-    public String getRef()
-    {
-      return ref;
+    public List<CommentType.Link> getLink() {
+        if (link == null) {
+            link = new ArrayList<CommentType.Link>();
+        }
+        return this.link;
     }
 
     /**
-     * Sets the value of the ref property.
+     * Gets the value of the event property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the event property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getEvent().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link EventType }
      * 
-     * @param value
-     *          allowed object is {@link String }
      * 
      */
-    public void setRef(String value)
-    {
-      this.ref = value;
+    public List<EventType> getEvent() {
+        if (event == null) {
+            event = new ArrayList<EventType>();
+        }
+        return this.event;
     }
 
     /**
-     * <p>
-     * Java class for anonymous complex type.
+     * Gets the value of the isoform property.
      * 
      * <p>
-     * The following schema fragment specifies the expected content contained
-     * within this class.
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the isoform property.
      * 
+     * <p>
+     * For example, to add a new item, do as follows:
      * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;attribute name="resource" use="required">
-     *         &lt;simpleType>
-     *           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
-     *             &lt;enumeration value="EMBL-CDS"/>
-     *             &lt;enumeration value="EMBL"/>
-     *           &lt;/restriction>
-     *         &lt;/simpleType>
-     *       &lt;/attribute>
-     *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
+     *    getIsoform().add(newItem);
      * </pre>
      * 
      * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link IsoformType }
+     * 
+     * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class Sequence
-    {
-
-      @XmlAttribute(name = "resource", required = true)
-      protected String resource;
-
-      @XmlAttribute(name = "id", required = true)
-      protected String id;
-
-      @XmlAttribute(name = "version")
-      protected Integer version;
-
-      /**
-       * Gets the value of the resource property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getResource()
-      {
-        return resource;
-      }
-
-      /**
-       * Sets the value of the resource property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setResource(String value)
-      {
-        this.resource = value;
-      }
-
-      /**
-       * Gets the value of the id property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getId()
-      {
-        return id;
-      }
-
-      /**
-       * Sets the value of the id property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setId(String value)
-      {
-        this.id = value;
-      }
-
-      /**
-       * Gets the value of the version property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getVersion()
-      {
-        return version;
-      }
-
-      /**
-       * Sets the value of the version property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setVersion(Integer value)
-      {
-        this.version = value;
-      }
-
+    public List<IsoformType> getIsoform() {
+        if (isoform == null) {
+            isoform = new ArrayList<IsoformType>();
+        }
+        return this.isoform;
     }
 
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;sequence>
-   *         &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/>
-   *         &lt;element name="acronym" type="{http://www.w3.org/2001/XMLSchema}string"/>
-   *         &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/>
-   *         &lt;element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
-   *       &lt;/sequence>
-   *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(
-    name = "",
-    propOrder =
-    { "name", "acronym", "description", "dbReference" })
-  public static class Disease
-  {
-
-    @XmlElement(required = true)
-    protected String name;
-
-    @XmlElement(required = true)
-    protected String acronym;
+    /**
+     * Gets the value of the interactant property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the interactant property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getInteractant().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link InteractantType }
+     * 
+     * 
+     */
+    public List<InteractantType> getInteractant() {
+        if (interactant == null) {
+            interactant = new ArrayList<InteractantType>();
+        }
+        return this.interactant;
+    }
 
-    @XmlElement(required = true)
-    protected String description;
+    /**
+     * Gets the value of the organismsDiffer property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public Boolean isOrganismsDiffer() {
+        return organismsDiffer;
+    }
 
-    @XmlElement(required = true)
-    protected DbReferenceType dbReference;
+    /**
+     * Sets the value of the organismsDiffer property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setOrganismsDiffer(Boolean value) {
+        this.organismsDiffer = value;
+    }
 
-    @XmlAttribute(name = "id", required = true)
-    protected String id;
+    /**
+     * Gets the value of the experiments property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
+     */
+    public Integer getExperiments() {
+        return experiments;
+    }
 
     /**
-     * Gets the value of the name property.
+     * Sets the value of the experiments property.
      * 
-     * @return possible object is {@link String }
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setExperiments(Integer value) {
+        this.experiments = value;
+    }
+
+    /**
+     * Gets the value of the disease property.
      * 
+     * @return
+     *     possible object is
+     *     {@link CommentType.Disease }
+     *     
      */
-    public String getName()
-    {
-      return name;
+    public CommentType.Disease getDisease() {
+        return disease;
     }
 
     /**
-     * Sets the value of the name property.
+     * Sets the value of the disease property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link CommentType.Disease }
+     *     
      */
-    public void setName(String value)
-    {
-      this.name = value;
+    public void setDisease(CommentType.Disease value) {
+        this.disease = value;
     }
 
     /**
-     * Gets the value of the acronym property.
+     * Gets the value of the location property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the location property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getLocation().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link LocationType }
      * 
-     * @return possible object is {@link String }
      * 
      */
-    public String getAcronym()
-    {
-      return acronym;
+    public List<LocationType> getLocation() {
+        if (location == null) {
+            location = new ArrayList<LocationType>();
+        }
+        return this.location;
     }
 
     /**
-     * Sets the value of the acronym property.
+     * Gets the value of the text property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the text property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getText().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link EvidencedStringType }
      * 
-     * @param value
-     *          allowed object is {@link String }
      * 
      */
-    public void setAcronym(String value)
-    {
-      this.acronym = value;
+    public List<EvidencedStringType> getText() {
+        if (text == null) {
+            text = new ArrayList<EvidencedStringType>();
+        }
+        return this.text;
     }
 
     /**
-     * Gets the value of the description property.
-     * 
-     * @return possible object is {@link String }
+     * Gets the value of the type property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getDescription()
-    {
-      return description;
+    public String getType() {
+        return type;
     }
 
     /**
-     * Sets the value of the description property.
+     * Sets the value of the type property.
      * 
      * @param value
-     *          allowed object is {@link String }
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
+
+    /**
+     * Gets the value of the locationType property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public void setDescription(String value)
-    {
-      this.description = value;
+    public String getLocationType() {
+        return locationType;
     }
 
     /**
-     * Gets the value of the dbReference property.
+     * Sets the value of the locationType property.
      * 
-     * @return possible object is {@link DbReferenceType }
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setLocationType(String value) {
+        this.locationType = value;
+    }
+
+    /**
+     * Gets the value of the name property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public DbReferenceType getDbReference()
-    {
-      return dbReference;
+    public String getName() {
+        return name;
     }
 
     /**
-     * Sets the value of the dbReference property.
+     * Sets the value of the name property.
      * 
      * @param value
-     *          allowed object is {@link DbReferenceType }
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setName(String value) {
+        this.name = value;
+    }
+
+    /**
+     * Gets the value of the mass property.
      * 
+     * @return
+     *     possible object is
+     *     {@link Float }
+     *     
      */
-    public void setDbReference(DbReferenceType value)
-    {
-      this.dbReference = value;
+    public Float getMass() {
+        return mass;
     }
 
     /**
-     * Gets the value of the id property.
+     * Sets the value of the mass property.
      * 
-     * @return possible object is {@link String }
+     * @param value
+     *     allowed object is
+     *     {@link Float }
+     *     
+     */
+    public void setMass(Float value) {
+        this.mass = value;
+    }
+
+    /**
+     * Gets the value of the error property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getId()
-    {
-      return id;
+    public String getError() {
+        return error;
     }
 
     /**
-     * Sets the value of the id property.
+     * Sets the value of the error property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setId(String value)
-    {
-      this.id = value;
+    public void setError(String value) {
+        this.error = value;
     }
 
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;sequence>
-   *         &lt;element name="KM" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-   *         &lt;element name="Vmax" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-   *         &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-   *       &lt;/sequence>
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "km", "vmax", "text" })
-  public static class Kinetics
-  {
-
-    @XmlElement(name = "KM")
-    protected List<EvidencedStringType> km;
-
-    @XmlElement(name = "Vmax")
-    protected List<EvidencedStringType> vmax;
+    /**
+     * Gets the value of the method property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getMethod() {
+        return method;
+    }
 
-    protected List<EvidencedStringType> text;
+    /**
+     * Sets the value of the method property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setMethod(String value) {
+        this.method = value;
+    }
 
     /**
-     * Gets the value of the km property.
+     * Gets the value of the evidence property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the km property.
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the evidence property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
-     * 
      * <pre>
-     * getKM().add(newItem);
+     *    getEvidence().add(newItem);
      * </pre>
      * 
      * 
      * <p>
      * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
+     * {@link Integer }
      * 
      * 
      */
-    public List<EvidencedStringType> getKM()
-    {
-      if (km == null)
-      {
-        km = new ArrayList<EvidencedStringType>();
-      }
-      return this.km;
+    public List<Integer> getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList<Integer>();
+        }
+        return this.evidence;
     }
 
+
     /**
-     * Gets the value of the vmax property.
+     * <p>Java class for anonymous complex type.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the vmax property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * <p>The following schema fragment specifies the expected content contained within this class.
      * 
      * <pre>
-     * getVmax().add(newItem);
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="max" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
+     *         &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+     *       &lt;/sequence>
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
      * </pre>
      * 
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
-     * 
-     * 
      */
-    public List<EvidencedStringType> getVmax()
-    {
-      if (vmax == null)
-      {
-        vmax = new ArrayList<EvidencedStringType>();
-      }
-      return this.vmax;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "max",
+        "text"
+    })
+    public static class Absorption {
+
+        protected EvidencedStringType max;
+        protected List<EvidencedStringType> text;
+
+        /**
+         * Gets the value of the max property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public EvidencedStringType getMax() {
+            return max;
+        }
+
+        /**
+         * Sets the value of the max property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public void setMax(EvidencedStringType value) {
+            this.max = value;
+        }
+
+        /**
+         * Gets the value of the text property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the text property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getText().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List<EvidencedStringType> getText() {
+            if (text == null) {
+                text = new ArrayList<EvidencedStringType>();
+            }
+            return this.text;
+        }
+
     }
 
+
     /**
-     * Gets the value of the text property.
+     * <p>Java class for anonymous complex type.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the text property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * <p>The following schema fragment specifies the expected content contained within this class.
      * 
      * <pre>
-     * getText().add(newItem);
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="sequence" minOccurs="0">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 &lt;attribute name="resource" use="required">
+     *                   &lt;simpleType>
+     *                     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
+     *                       &lt;enumeration value="EMBL-CDS"/>
+     *                       &lt;enumeration value="EMBL"/>
+     *                     &lt;/restriction>
+     *                   &lt;/simpleType>
+     *                 &lt;/attribute>
+     *                 &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *               &lt;/restriction>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *       &lt;/sequence>
+     *       &lt;attribute name="type" use="required">
+     *         &lt;simpleType>
+     *           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
+     *             &lt;enumeration value="frameshift"/>
+     *             &lt;enumeration value="erroneous initiation"/>
+     *             &lt;enumeration value="erroneous termination"/>
+     *             &lt;enumeration value="erroneous gene model prediction"/>
+     *             &lt;enumeration value="erroneous translation"/>
+     *             &lt;enumeration value="miscellaneous discrepancy"/>
+     *           &lt;/restriction>
+     *         &lt;/simpleType>
+     *       &lt;/attribute>
+     *       &lt;attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
      * </pre>
      * 
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
-     * 
-     * 
      */
-    public List<EvidencedStringType> getText()
-    {
-      if (text == null)
-      {
-        text = new ArrayList<EvidencedStringType>();
-      }
-      return this.text;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "sequence"
+    })
+    public static class Conflict {
+
+        protected CommentType.Conflict.Sequence sequence;
+        @XmlAttribute(name = "type", required = true)
+        protected String type;
+        @XmlAttribute(name = "ref")
+        protected String ref;
+
+        /**
+         * Gets the value of the sequence property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link CommentType.Conflict.Sequence }
+         *     
+         */
+        public CommentType.Conflict.Sequence getSequence() {
+            return sequence;
+        }
+
+        /**
+         * Sets the value of the sequence property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link CommentType.Conflict.Sequence }
+         *     
+         */
+        public void setSequence(CommentType.Conflict.Sequence value) {
+            this.sequence = value;
+        }
+
+        /**
+         * Gets the value of the type property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getType() {
+            return type;
+        }
+
+        /**
+         * Sets the value of the type property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setType(String value) {
+            this.type = value;
+        }
+
+        /**
+         * Gets the value of the ref property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getRef() {
+            return ref;
+        }
+
+        /**
+         * Sets the value of the ref property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setRef(String value) {
+            this.ref = value;
+        }
+
+
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       &lt;attribute name="resource" use="required">
+         *         &lt;simpleType>
+         *           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
+         *             &lt;enumeration value="EMBL-CDS"/>
+         *             &lt;enumeration value="EMBL"/>
+         *           &lt;/restriction>
+         *         &lt;/simpleType>
+         *       &lt;/attribute>
+         *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *     &lt;/restriction>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class Sequence {
+
+            @XmlAttribute(name = "resource", required = true)
+            protected String resource;
+            @XmlAttribute(name = "id", required = true)
+            protected String id;
+            @XmlAttribute(name = "version")
+            protected Integer version;
+
+            /**
+             * Gets the value of the resource property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getResource() {
+                return resource;
+            }
+
+            /**
+             * Sets the value of the resource property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setResource(String value) {
+                this.resource = value;
+            }
+
+            /**
+             * Gets the value of the id property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getId() {
+                return id;
+            }
+
+            /**
+             * Sets the value of the id property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setId(String value) {
+                this.id = value;
+            }
+
+            /**
+             * Gets the value of the version property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getVersion() {
+                return version;
+            }
+
+            /**
+             * Sets the value of the version property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setVersion(Integer value) {
+                this.version = value;
+            }
+
+        }
+
     }
 
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;attribute name="uri" use="required" type="{http://www.w3.org/2001/XMLSchema}anyURI" />
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class Link
-  {
-
-    @XmlAttribute(name = "uri", required = true)
-    @XmlSchemaType(name = "anyURI")
-    protected String uri;
 
     /**
-     * Gets the value of the uri property.
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/>
+     *         &lt;element name="acronym" type="{http://www.w3.org/2001/XMLSchema}string"/>
+     *         &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/>
+     *         &lt;element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
+     *       &lt;/sequence>
+     *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
      * 
-     * @return possible object is {@link String }
      * 
      */
-    public String getUri()
-    {
-      return uri;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "name",
+        "acronym",
+        "description",
+        "dbReference"
+    })
+    public static class Disease {
+
+        @XmlElement(required = true)
+        protected String name;
+        @XmlElement(required = true)
+        protected String acronym;
+        @XmlElement(required = true)
+        protected String description;
+        @XmlElement(required = true)
+        protected DbReferenceType dbReference;
+        @XmlAttribute(name = "id", required = true)
+        protected String id;
+
+        /**
+         * Gets the value of the name property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getName() {
+            return name;
+        }
+
+        /**
+         * Sets the value of the name property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setName(String value) {
+            this.name = value;
+        }
+
+        /**
+         * Gets the value of the acronym property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getAcronym() {
+            return acronym;
+        }
+
+        /**
+         * Sets the value of the acronym property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setAcronym(String value) {
+            this.acronym = value;
+        }
+
+        /**
+         * Gets the value of the description property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getDescription() {
+            return description;
+        }
+
+        /**
+         * Sets the value of the description property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setDescription(String value) {
+            this.description = value;
+        }
+
+        /**
+         * Gets the value of the dbReference property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link DbReferenceType }
+         *     
+         */
+        public DbReferenceType getDbReference() {
+            return dbReference;
+        }
+
+        /**
+         * Sets the value of the dbReference property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link DbReferenceType }
+         *     
+         */
+        public void setDbReference(DbReferenceType value) {
+            this.dbReference = value;
+        }
+
+        /**
+         * Gets the value of the id property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getId() {
+            return id;
+        }
+
+        /**
+         * Sets the value of the id property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setId(String value) {
+            this.id = value;
+        }
+
     }
 
+
     /**
-     * Sets the value of the uri property.
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="KM" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+     *         &lt;element name="Vmax" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+     *         &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+     *       &lt;/sequence>
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
      * 
-     * @param value
-     *          allowed object is {@link String }
      * 
      */
-    public void setUri(String value)
-    {
-      this.uri = value;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "km",
+        "vmax",
+        "text"
+    })
+    public static class Kinetics {
+
+        @XmlElement(name = "KM")
+        protected List<EvidencedStringType> km;
+        @XmlElement(name = "Vmax")
+        protected List<EvidencedStringType> vmax;
+        protected List<EvidencedStringType> text;
+
+        /**
+         * Gets the value of the km property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the km property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getKM().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List<EvidencedStringType> getKM() {
+            if (km == null) {
+                km = new ArrayList<EvidencedStringType>();
+            }
+            return this.km;
+        }
+
+        /**
+         * Gets the value of the vmax property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the vmax property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getVmax().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List<EvidencedStringType> getVmax() {
+            if (vmax == null) {
+                vmax = new ArrayList<EvidencedStringType>();
+            }
+            return this.vmax;
+        }
+
+        /**
+         * Gets the value of the text property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the text property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getText().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List<EvidencedStringType> getText() {
+            if (text == null) {
+                text = new ArrayList<EvidencedStringType>();
+            }
+            return this.text;
+        }
+
     }
 
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;sequence>
-   *         &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
-   *       &lt;/sequence>
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "text" })
-  public static class PhDependence
-  {
-
-    @XmlElement(required = true)
-    protected List<EvidencedStringType> text;
 
     /**
-     * Gets the value of the text property.
+     * <p>Java class for anonymous complex type.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the text property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * <p>The following schema fragment specifies the expected content contained within this class.
      * 
      * <pre>
-     * getText().add(newItem);
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attribute name="uri" use="required" type="{http://www.w3.org/2001/XMLSchema}anyURI" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
      * </pre>
      * 
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
-     * 
-     * 
      */
-    public List<EvidencedStringType> getText()
-    {
-      if (text == null)
-      {
-        text = new ArrayList<EvidencedStringType>();
-      }
-      return this.text;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class Link {
+
+        @XmlAttribute(name = "uri", required = true)
+        @XmlSchemaType(name = "anyURI")
+        protected String uri;
+
+        /**
+         * Gets the value of the uri property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getUri() {
+            return uri;
+        }
+
+        /**
+         * Sets the value of the uri property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setUri(String value) {
+            this.uri = value;
+        }
+
     }
 
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;sequence>
-   *         &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
-   *       &lt;/sequence>
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "text" })
-  public static class RedoxPotential
-  {
-
-    @XmlElement(required = true)
-    protected List<EvidencedStringType> text;
 
     /**
-     * Gets the value of the text property.
+     * <p>Java class for anonymous complex type.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the text property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * <p>The following schema fragment specifies the expected content contained within this class.
      * 
      * <pre>
-     * getText().add(newItem);
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+     *       &lt;/sequence>
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
      * </pre>
      * 
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
-     * 
-     * 
      */
-    public List<EvidencedStringType> getText()
-    {
-      if (text == null)
-      {
-        text = new ArrayList<EvidencedStringType>();
-      }
-      return this.text;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "text"
+    })
+    public static class PhDependence {
+
+        @XmlElement(required = true)
+        protected List<EvidencedStringType> text;
+
+        /**
+         * Gets the value of the text property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the text property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getText().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List<EvidencedStringType> getText() {
+            if (text == null) {
+                text = new ArrayList<EvidencedStringType>();
+            }
+            return this.text;
+        }
+
     }
 
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;sequence>
-   *         &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
-   *       &lt;/sequence>
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "text" })
-  public static class TemperatureDependence
-  {
-
-    @XmlElement(required = true)
-    protected List<EvidencedStringType> text;
 
     /**
-     * Gets the value of the text property.
+     * <p>Java class for anonymous complex type.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the text property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * <p>The following schema fragment specifies the expected content contained within this class.
      * 
      * <pre>
-     * getText().add(newItem);
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+     *       &lt;/sequence>
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
      * </pre>
      * 
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "text"
+    })
+    public static class RedoxPotential {
+
+        @XmlElement(required = true)
+        protected List<EvidencedStringType> text;
+
+        /**
+         * Gets the value of the text property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the text property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getText().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List<EvidencedStringType> getText() {
+            if (text == null) {
+                text = new ArrayList<EvidencedStringType>();
+            }
+            return this.text;
+        }
+
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+     *       &lt;/sequence>
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
      * 
      * 
      */
-    public List<EvidencedStringType> getText()
-    {
-      if (text == null)
-      {
-        text = new ArrayList<EvidencedStringType>();
-      }
-      return this.text;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "text"
+    })
+    public static class TemperatureDependence {
+
+        @XmlElement(required = true)
+        protected List<EvidencedStringType> text;
+
+        /**
+         * Gets the value of the text property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the text property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getText().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List<EvidencedStringType> getText() {
+            if (text == null) {
+                text = new ArrayList<EvidencedStringType>();
+            }
+            return this.text;
+        }
 
-  }
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/ConsortiumType.java b/src/jalview/xml/binding/uniprot/ConsortiumType.java
index 1b98b9b..e1b1db1 100644
--- a/src/jalview/xml/binding/uniprot/ConsortiumType.java
+++ b/src/jalview/xml/binding/uniprot/ConsortiumType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,16 +13,14 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes the authors of a citation when these are represented by a
- * consortium. Equivalent to the flat file RG-line.
+ * Describes the authors of a citation when these are represented by a consortium.
+ *             Equivalent to the flat file RG-line.
  * 
- * <p>
- * Java class for consortiumType complex type.
+ * <p>Java class for consortiumType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="consortiumType">
@@ -37,33 +36,33 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "consortiumType")
-public class ConsortiumType
-{
+public class ConsortiumType {
 
-  @XmlAttribute(name = "name", required = true)
-  protected String name;
+    @XmlAttribute(name = "name", required = true)
+    protected String name;
 
-  /**
-   * Gets the value of the name property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getName()
-  {
-    return name;
-  }
+    /**
+     * Gets the value of the name property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getName() {
+        return name;
+    }
 
-  /**
-   * Sets the value of the name property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setName(String value)
-  {
-    this.name = value;
-  }
+    /**
+     * Sets the value of the name property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setName(String value) {
+        this.name = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/DbReferenceType.java b/src/jalview/xml/binding/uniprot/DbReferenceType.java
index 84cbba7..9bfde39 100644
--- a/src/jalview/xml/binding/uniprot/DbReferenceType.java
+++ b/src/jalview/xml/binding/uniprot/DbReferenceType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -14,16 +15,15 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes a database cross-reference. Equivalent to the flat file DR-line.
+ * Describes a database cross-reference.
+ *             Equivalent to the flat file DR-line.
+ *             
  * 
+ * <p>Java class for dbReferenceType complex type.
  * 
- * <p>
- * Java class for dbReferenceType complex type.
- * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="dbReferenceType">
@@ -44,153 +44,149 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "dbReferenceType", propOrder = { "molecule", "property" })
-public class DbReferenceType
-{
-
-  protected MoleculeType molecule;
-
-  protected List<PropertyType> property;
-
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
-
-  @XmlAttribute(name = "id", required = true)
-  protected String id;
-
-  @XmlAttribute(name = "evidence")
-  protected List<Integer> evidence;
-
-  /**
-   * Gets the value of the molecule property.
-   * 
-   * @return possible object is {@link MoleculeType }
-   * 
-   */
-  public MoleculeType getMolecule()
-  {
-    return molecule;
-  }
+@XmlType(name = "dbReferenceType", propOrder = {
+    "molecule",
+    "property"
+})
+public class DbReferenceType {
+
+    protected MoleculeType molecule;
+    protected List<PropertyType> property;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
+    @XmlAttribute(name = "id", required = true)
+    protected String id;
+    @XmlAttribute(name = "evidence")
+    protected List<Integer> evidence;
+
+    /**
+     * Gets the value of the molecule property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link MoleculeType }
+     *     
+     */
+    public MoleculeType getMolecule() {
+        return molecule;
+    }
 
-  /**
-   * Sets the value of the molecule property.
-   * 
-   * @param value
-   *          allowed object is {@link MoleculeType }
-   * 
-   */
-  public void setMolecule(MoleculeType value)
-  {
-    this.molecule = value;
-  }
+    /**
+     * Sets the value of the molecule property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link MoleculeType }
+     *     
+     */
+    public void setMolecule(MoleculeType value) {
+        this.molecule = value;
+    }
 
-  /**
-   * Gets the value of the property property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the property property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getProperty().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link PropertyType }
-   * 
-   * 
-   */
-  public List<PropertyType> getProperty()
-  {
-    if (property == null)
-    {
-      property = new ArrayList<PropertyType>();
+    /**
+     * Gets the value of the property property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the property property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getProperty().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link PropertyType }
+     * 
+     * 
+     */
+    public List<PropertyType> getProperty() {
+        if (property == null) {
+            property = new ArrayList<PropertyType>();
+        }
+        return this.property;
     }
-    return this.property;
-  }
 
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
+    /**
+     * Gets the value of the type property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getType() {
+        return type;
+    }
 
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
+    /**
+     * Sets the value of the type property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
 
-  /**
-   * Gets the value of the id property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getId()
-  {
-    return id;
-  }
+    /**
+     * Gets the value of the id property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getId() {
+        return id;
+    }
 
-  /**
-   * Sets the value of the id property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setId(String value)
-  {
-    this.id = value;
-  }
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setId(String value) {
+        this.id = value;
+    }
 
-  /**
-   * Gets the value of the evidence property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the evidence property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getEvidence().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List<Integer> getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList<Integer>();
+    /**
+     * Gets the value of the evidence property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the evidence property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getEvidence().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link Integer }
+     * 
+     * 
+     */
+    public List<Integer> getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList<Integer>();
+        }
+        return this.evidence;
     }
-    return this.evidence;
-  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/Entry.java b/src/jalview/xml/binding/uniprot/Entry.java
index 65bbd88..8ca1da7 100644
--- a/src/jalview/xml/binding/uniprot/Entry.java
+++ b/src/jalview/xml/binding/uniprot/Entry.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -18,13 +19,11 @@ import javax.xml.bind.annotation.XmlSchemaType;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.datatype.XMLGregorianCalendar;
 
+
 /**
- * <p>
- * Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType>
@@ -66,594 +65,561 @@ import javax.xml.datatype.XMLGregorianCalendar;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "",
-  propOrder =
-  { "accession", "name", "protein", "gene", "organism", "organismHost",
-      "geneLocation", "reference", "comment", "dbReference",
-      "proteinExistence", "keyword", "feature", "evidence", "sequence" })
+@XmlType(name = "", propOrder = {
+    "accession",
+    "name",
+    "protein",
+    "gene",
+    "organism",
+    "organismHost",
+    "geneLocation",
+    "reference",
+    "comment",
+    "dbReference",
+    "proteinExistence",
+    "keyword",
+    "feature",
+    "evidence",
+    "sequence"
+})
 @XmlRootElement(name = "entry")
-public class Entry
-{
-
-  @XmlElement(required = true)
-  protected List<String> accession;
-
-  @XmlElement(required = true)
-  protected List<String> name;
-
-  @XmlElement(required = true)
-  protected ProteinType protein;
-
-  protected List<GeneType> gene;
+public class Entry {
+
+    @XmlElement(required = true)
+    protected List<String> accession;
+    @XmlElement(required = true)
+    protected List<String> name;
+    @XmlElement(required = true)
+    protected ProteinType protein;
+    protected List<GeneType> gene;
+    @XmlElement(required = true)
+    protected OrganismType organism;
+    protected List<OrganismType> organismHost;
+    protected List<GeneLocationType> geneLocation;
+    @XmlElement(required = true)
+    protected List<ReferenceType> reference;
+    @XmlElement(nillable = true)
+    protected List<CommentType> comment;
+    protected List<DbReferenceType> dbReference;
+    @XmlElement(required = true)
+    protected ProteinExistenceType proteinExistence;
+    protected List<KeywordType> keyword;
+    protected List<FeatureType> feature;
+    protected List<EvidenceType> evidence;
+    @XmlElement(required = true)
+    protected SequenceType sequence;
+    @XmlAttribute(name = "dataset", required = true)
+    protected String dataset;
+    @XmlAttribute(name = "created", required = true)
+    @XmlSchemaType(name = "date")
+    protected XMLGregorianCalendar created;
+    @XmlAttribute(name = "modified", required = true)
+    @XmlSchemaType(name = "date")
+    protected XMLGregorianCalendar modified;
+    @XmlAttribute(name = "version", required = true)
+    protected int version;
+
+    /**
+     * Gets the value of the accession property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the accession property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getAccession().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
+     * 
+     */
+    public List<String> getAccession() {
+        if (accession == null) {
+            accession = new ArrayList<String>();
+        }
+        return this.accession;
+    }
 
-  @XmlElement(required = true)
-  protected OrganismType organism;
+    /**
+     * Gets the value of the name property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the name property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getName().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
+     * 
+     */
+    public List<String> getName() {
+        if (name == null) {
+            name = new ArrayList<String>();
+        }
+        return this.name;
+    }
 
-  protected List<OrganismType> organismHost;
+    /**
+     * Gets the value of the protein property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link ProteinType }
+     *     
+     */
+    public ProteinType getProtein() {
+        return protein;
+    }
 
-  protected List<GeneLocationType> geneLocation;
+    /**
+     * Sets the value of the protein property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link ProteinType }
+     *     
+     */
+    public void setProtein(ProteinType value) {
+        this.protein = value;
+    }
 
-  @XmlElement(required = true)
-  protected List<ReferenceType> reference;
+    /**
+     * Gets the value of the gene property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the gene property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getGene().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link GeneType }
+     * 
+     * 
+     */
+    public List<GeneType> getGene() {
+        if (gene == null) {
+            gene = new ArrayList<GeneType>();
+        }
+        return this.gene;
+    }
 
-  @XmlElement(nillable = true)
-  protected List<CommentType> comment;
+    /**
+     * Gets the value of the organism property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link OrganismType }
+     *     
+     */
+    public OrganismType getOrganism() {
+        return organism;
+    }
 
-  protected List<DbReferenceType> dbReference;
+    /**
+     * Sets the value of the organism property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link OrganismType }
+     *     
+     */
+    public void setOrganism(OrganismType value) {
+        this.organism = value;
+    }
 
-  @XmlElement(required = true)
-  protected ProteinExistenceType proteinExistence;
+    /**
+     * Gets the value of the organismHost property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the organismHost property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getOrganismHost().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link OrganismType }
+     * 
+     * 
+     */
+    public List<OrganismType> getOrganismHost() {
+        if (organismHost == null) {
+            organismHost = new ArrayList<OrganismType>();
+        }
+        return this.organismHost;
+    }
 
-  protected List<KeywordType> keyword;
+    /**
+     * Gets the value of the geneLocation property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the geneLocation property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getGeneLocation().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link GeneLocationType }
+     * 
+     * 
+     */
+    public List<GeneLocationType> getGeneLocation() {
+        if (geneLocation == null) {
+            geneLocation = new ArrayList<GeneLocationType>();
+        }
+        return this.geneLocation;
+    }
 
-  protected List<FeatureType> feature;
+    /**
+     * Gets the value of the reference property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the reference property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getReference().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link ReferenceType }
+     * 
+     * 
+     */
+    public List<ReferenceType> getReference() {
+        if (reference == null) {
+            reference = new ArrayList<ReferenceType>();
+        }
+        return this.reference;
+    }
 
-  protected List<EvidenceType> evidence;
+    /**
+     * Gets the value of the comment property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the comment property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getComment().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link CommentType }
+     * 
+     * 
+     */
+    public List<CommentType> getComment() {
+        if (comment == null) {
+            comment = new ArrayList<CommentType>();
+        }
+        return this.comment;
+    }
 
-  @XmlElement(required = true)
-  protected SequenceType sequence;
+    /**
+     * Gets the value of the dbReference property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the dbReference property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getDbReference().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link DbReferenceType }
+     * 
+     * 
+     */
+    public List<DbReferenceType> getDbReference() {
+        if (dbReference == null) {
+            dbReference = new ArrayList<DbReferenceType>();
+        }
+        return this.dbReference;
+    }
 
-  @XmlAttribute(name = "dataset", required = true)
-  protected String dataset;
+    /**
+     * Gets the value of the proteinExistence property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link ProteinExistenceType }
+     *     
+     */
+    public ProteinExistenceType getProteinExistence() {
+        return proteinExistence;
+    }
 
-  @XmlAttribute(name = "created", required = true)
-  @XmlSchemaType(name = "date")
-  protected XMLGregorianCalendar created;
+    /**
+     * Sets the value of the proteinExistence property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link ProteinExistenceType }
+     *     
+     */
+    public void setProteinExistence(ProteinExistenceType value) {
+        this.proteinExistence = value;
+    }
 
-  @XmlAttribute(name = "modified", required = true)
-  @XmlSchemaType(name = "date")
-  protected XMLGregorianCalendar modified;
+    /**
+     * Gets the value of the keyword property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the keyword property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getKeyword().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link KeywordType }
+     * 
+     * 
+     */
+    public List<KeywordType> getKeyword() {
+        if (keyword == null) {
+            keyword = new ArrayList<KeywordType>();
+        }
+        return this.keyword;
+    }
 
-  @XmlAttribute(name = "version", required = true)
-  protected int version;
+    /**
+     * Gets the value of the feature property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the feature property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getFeature().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link FeatureType }
+     * 
+     * 
+     */
+    public List<FeatureType> getFeature() {
+        if (feature == null) {
+            feature = new ArrayList<FeatureType>();
+        }
+        return this.feature;
+    }
 
-  /**
-   * Gets the value of the accession property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the accession property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getAccession().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link String }
-   * 
-   * 
-   */
-  public List<String> getAccession()
-  {
-    if (accession == null)
-    {
-      accession = new ArrayList<String>();
+    /**
+     * Gets the value of the evidence property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the evidence property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getEvidence().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link EvidenceType }
+     * 
+     * 
+     */
+    public List<EvidenceType> getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList<EvidenceType>();
+        }
+        return this.evidence;
     }
-    return this.accession;
-  }
-
-  /**
-   * Gets the value of the name property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the name property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getName().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link String }
-   * 
-   * 
-   */
-  public List<String> getName()
-  {
-    if (name == null)
-    {
-      name = new ArrayList<String>();
+
+    /**
+     * Gets the value of the sequence property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link SequenceType }
+     *     
+     */
+    public SequenceType getSequence() {
+        return sequence;
     }
-    return this.name;
-  }
-
-  /**
-   * Gets the value of the protein property.
-   * 
-   * @return possible object is {@link ProteinType }
-   * 
-   */
-  public ProteinType getProtein()
-  {
-    return protein;
-  }
-
-  /**
-   * Sets the value of the protein property.
-   * 
-   * @param value
-   *          allowed object is {@link ProteinType }
-   * 
-   */
-  public void setProtein(ProteinType value)
-  {
-    this.protein = value;
-  }
-
-  /**
-   * Gets the value of the gene property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the gene property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getGene().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link GeneType }
-   * 
-   * 
-   */
-  public List<GeneType> getGene()
-  {
-    if (gene == null)
-    {
-      gene = new ArrayList<GeneType>();
+
+    /**
+     * Sets the value of the sequence property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link SequenceType }
+     *     
+     */
+    public void setSequence(SequenceType value) {
+        this.sequence = value;
     }
-    return this.gene;
-  }
-
-  /**
-   * Gets the value of the organism property.
-   * 
-   * @return possible object is {@link OrganismType }
-   * 
-   */
-  public OrganismType getOrganism()
-  {
-    return organism;
-  }
-
-  /**
-   * Sets the value of the organism property.
-   * 
-   * @param value
-   *          allowed object is {@link OrganismType }
-   * 
-   */
-  public void setOrganism(OrganismType value)
-  {
-    this.organism = value;
-  }
-
-  /**
-   * Gets the value of the organismHost property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the organismHost property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getOrganismHost().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link OrganismType }
-   * 
-   * 
-   */
-  public List<OrganismType> getOrganismHost()
-  {
-    if (organismHost == null)
-    {
-      organismHost = new ArrayList<OrganismType>();
+
+    /**
+     * Gets the value of the dataset property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDataset() {
+        return dataset;
     }
-    return this.organismHost;
-  }
-
-  /**
-   * Gets the value of the geneLocation property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the geneLocation property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getGeneLocation().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link GeneLocationType }
-   * 
-   * 
-   */
-  public List<GeneLocationType> getGeneLocation()
-  {
-    if (geneLocation == null)
-    {
-      geneLocation = new ArrayList<GeneLocationType>();
+
+    /**
+     * Sets the value of the dataset property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDataset(String value) {
+        this.dataset = value;
     }
-    return this.geneLocation;
-  }
-
-  /**
-   * Gets the value of the reference property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the reference property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getReference().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link ReferenceType }
-   * 
-   * 
-   */
-  public List<ReferenceType> getReference()
-  {
-    if (reference == null)
-    {
-      reference = new ArrayList<ReferenceType>();
+
+    /**
+     * Gets the value of the created property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link XMLGregorianCalendar }
+     *     
+     */
+    public XMLGregorianCalendar getCreated() {
+        return created;
     }
-    return this.reference;
-  }
-
-  /**
-   * Gets the value of the comment property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the comment property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getComment().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link CommentType
-   * }
-   * 
-   * 
-   */
-  public List<CommentType> getComment()
-  {
-    if (comment == null)
-    {
-      comment = new ArrayList<CommentType>();
+
+    /**
+     * Sets the value of the created property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link XMLGregorianCalendar }
+     *     
+     */
+    public void setCreated(XMLGregorianCalendar value) {
+        this.created = value;
     }
-    return this.comment;
-  }
-
-  /**
-   * Gets the value of the dbReference property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the dbReference property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getDbReference().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link DbReferenceType }
-   * 
-   * 
-   */
-  public List<DbReferenceType> getDbReference()
-  {
-    if (dbReference == null)
-    {
-      dbReference = new ArrayList<DbReferenceType>();
+
+    /**
+     * Gets the value of the modified property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link XMLGregorianCalendar }
+     *     
+     */
+    public XMLGregorianCalendar getModified() {
+        return modified;
     }
-    return this.dbReference;
-  }
-
-  /**
-   * Gets the value of the proteinExistence property.
-   * 
-   * @return possible object is {@link ProteinExistenceType }
-   * 
-   */
-  public ProteinExistenceType getProteinExistence()
-  {
-    return proteinExistence;
-  }
-
-  /**
-   * Sets the value of the proteinExistence property.
-   * 
-   * @param value
-   *          allowed object is {@link ProteinExistenceType }
-   * 
-   */
-  public void setProteinExistence(ProteinExistenceType value)
-  {
-    this.proteinExistence = value;
-  }
-
-  /**
-   * Gets the value of the keyword property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the keyword property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getKeyword().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link KeywordType
-   * }
-   * 
-   * 
-   */
-  public List<KeywordType> getKeyword()
-  {
-    if (keyword == null)
-    {
-      keyword = new ArrayList<KeywordType>();
+
+    /**
+     * Sets the value of the modified property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link XMLGregorianCalendar }
+     *     
+     */
+    public void setModified(XMLGregorianCalendar value) {
+        this.modified = value;
     }
-    return this.keyword;
-  }
-
-  /**
-   * Gets the value of the feature property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the feature property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getFeature().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link FeatureType
-   * }
-   * 
-   * 
-   */
-  public List<FeatureType> getFeature()
-  {
-    if (feature == null)
-    {
-      feature = new ArrayList<FeatureType>();
+
+    /**
+     * Gets the value of the version property.
+     * 
+     */
+    public int getVersion() {
+        return version;
     }
-    return this.feature;
-  }
-
-  /**
-   * Gets the value of the evidence property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the evidence property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getEvidence().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link EvidenceType }
-   * 
-   * 
-   */
-  public List<EvidenceType> getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList<EvidenceType>();
+
+    /**
+     * Sets the value of the version property.
+     * 
+     */
+    public void setVersion(int value) {
+        this.version = value;
     }
-    return this.evidence;
-  }
-
-  /**
-   * Gets the value of the sequence property.
-   * 
-   * @return possible object is {@link SequenceType }
-   * 
-   */
-  public SequenceType getSequence()
-  {
-    return sequence;
-  }
-
-  /**
-   * Sets the value of the sequence property.
-   * 
-   * @param value
-   *          allowed object is {@link SequenceType }
-   * 
-   */
-  public void setSequence(SequenceType value)
-  {
-    this.sequence = value;
-  }
-
-  /**
-   * Gets the value of the dataset property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDataset()
-  {
-    return dataset;
-  }
-
-  /**
-   * Sets the value of the dataset property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDataset(String value)
-  {
-    this.dataset = value;
-  }
-
-  /**
-   * Gets the value of the created property.
-   * 
-   * @return possible object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public XMLGregorianCalendar getCreated()
-  {
-    return created;
-  }
-
-  /**
-   * Sets the value of the created property.
-   * 
-   * @param value
-   *          allowed object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public void setCreated(XMLGregorianCalendar value)
-  {
-    this.created = value;
-  }
-
-  /**
-   * Gets the value of the modified property.
-   * 
-   * @return possible object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public XMLGregorianCalendar getModified()
-  {
-    return modified;
-  }
-
-  /**
-   * Sets the value of the modified property.
-   * 
-   * @param value
-   *          allowed object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public void setModified(XMLGregorianCalendar value)
-  {
-    this.modified = value;
-  }
-
-  /**
-   * Gets the value of the version property.
-   * 
-   */
-  public int getVersion()
-  {
-    return version;
-  }
-
-  /**
-   * Sets the value of the version property.
-   * 
-   */
-  public void setVersion(int value)
-  {
-    this.version = value;
-  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/EventType.java b/src/jalview/xml/binding/uniprot/EventType.java
index d3fe7f9..44566fe 100644
--- a/src/jalview/xml/binding/uniprot/EventType.java
+++ b/src/jalview/xml/binding/uniprot/EventType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,15 +13,13 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
  * Describes the type of events that cause alternative products.
  * 
- * <p>
- * Java class for eventType complex type.
+ * <p>Java class for eventType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="eventType">
@@ -45,33 +44,33 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "eventType")
-public class EventType
-{
+public class EventType {
 
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
 
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
+    /**
+     * Gets the value of the type property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getType() {
+        return type;
+    }
 
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
+    /**
+     * Sets the value of the type property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/EvidenceType.java b/src/jalview/xml/binding/uniprot/EvidenceType.java
index 6e0ff99..371a778 100644
--- a/src/jalview/xml/binding/uniprot/EvidenceType.java
+++ b/src/jalview/xml/binding/uniprot/EvidenceType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.math.BigInteger;
@@ -13,15 +14,14 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes the evidence for an annotation. No flat file equivalent.
+ * Describes the evidence for an annotation.
+ *             No flat file equivalent.
  * 
- * <p>
- * Java class for evidenceType complex type.
+ * <p>Java class for evidenceType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="evidenceType">
@@ -41,110 +41,113 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "evidenceType", propOrder = { "source", "importedFrom" })
-public class EvidenceType
-{
-
-  protected SourceType source;
-
-  protected ImportedFromType importedFrom;
-
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
-
-  @XmlAttribute(name = "key", required = true)
-  protected BigInteger key;
-
-  /**
-   * Gets the value of the source property.
-   * 
-   * @return possible object is {@link SourceType }
-   * 
-   */
-  public SourceType getSource()
-  {
-    return source;
-  }
-
-  /**
-   * Sets the value of the source property.
-   * 
-   * @param value
-   *          allowed object is {@link SourceType }
-   * 
-   */
-  public void setSource(SourceType value)
-  {
-    this.source = value;
-  }
-
-  /**
-   * Gets the value of the importedFrom property.
-   * 
-   * @return possible object is {@link ImportedFromType }
-   * 
-   */
-  public ImportedFromType getImportedFrom()
-  {
-    return importedFrom;
-  }
-
-  /**
-   * Sets the value of the importedFrom property.
-   * 
-   * @param value
-   *          allowed object is {@link ImportedFromType }
-   * 
-   */
-  public void setImportedFrom(ImportedFromType value)
-  {
-    this.importedFrom = value;
-  }
-
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
-
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
-
-  /**
-   * Gets the value of the key property.
-   * 
-   * @return possible object is {@link BigInteger }
-   * 
-   */
-  public BigInteger getKey()
-  {
-    return key;
-  }
-
-  /**
-   * Sets the value of the key property.
-   * 
-   * @param value
-   *          allowed object is {@link BigInteger }
-   * 
-   */
-  public void setKey(BigInteger value)
-  {
-    this.key = value;
-  }
+@XmlType(name = "evidenceType", propOrder = {
+    "source",
+    "importedFrom"
+})
+public class EvidenceType {
+
+    protected SourceType source;
+    protected ImportedFromType importedFrom;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
+    @XmlAttribute(name = "key", required = true)
+    protected BigInteger key;
+
+    /**
+     * Gets the value of the source property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link SourceType }
+     *     
+     */
+    public SourceType getSource() {
+        return source;
+    }
+
+    /**
+     * Sets the value of the source property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link SourceType }
+     *     
+     */
+    public void setSource(SourceType value) {
+        this.source = value;
+    }
+
+    /**
+     * Gets the value of the importedFrom property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link ImportedFromType }
+     *     
+     */
+    public ImportedFromType getImportedFrom() {
+        return importedFrom;
+    }
+
+    /**
+     * Sets the value of the importedFrom property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link ImportedFromType }
+     *     
+     */
+    public void setImportedFrom(ImportedFromType value) {
+        this.importedFrom = value;
+    }
+
+    /**
+     * Gets the value of the type property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getType() {
+        return type;
+    }
+
+    /**
+     * Sets the value of the type property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
+
+    /**
+     * Gets the value of the key property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link BigInteger }
+     *     
+     */
+    public BigInteger getKey() {
+        return key;
+    }
+
+    /**
+     * Sets the value of the key property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link BigInteger }
+     *     
+     */
+    public void setKey(BigInteger value) {
+        this.key = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/EvidencedStringType.java b/src/jalview/xml/binding/uniprot/EvidencedStringType.java
index 33e8c53..def955e 100644
--- a/src/jalview/xml/binding/uniprot/EvidencedStringType.java
+++ b/src/jalview/xml/binding/uniprot/EvidencedStringType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,13 +16,11 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
+
 /**
- * <p>
- * Java class for evidencedStringType complex type.
+ * <p>Java class for evidencedStringType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="evidencedStringType">
@@ -45,94 +44,93 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "evidencedStringType", propOrder = { "value" })
-public class EvidencedStringType
-{
-
-  @XmlValue
-  protected String value;
-
-  @XmlAttribute(name = "evidence")
-  protected List<Integer> evidence;
+@XmlType(name = "evidencedStringType", propOrder = {
+    "value"
+})
+public class EvidencedStringType {
 
-  @XmlAttribute(name = "status")
-  protected String status;
+    @XmlValue
+    protected String value;
+    @XmlAttribute(name = "evidence")
+    protected List<Integer> evidence;
+    @XmlAttribute(name = "status")
+    protected String status;
 
-  /**
-   * Gets the value of the value property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getValue()
-  {
-    return value;
-  }
+    /**
+     * Gets the value of the value property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getValue() {
+        return value;
+    }
 
-  /**
-   * Sets the value of the value property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setValue(String value)
-  {
-    this.value = value;
-  }
+    /**
+     * Sets the value of the value property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setValue(String value) {
+        this.value = value;
+    }
 
-  /**
-   * Gets the value of the evidence property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the evidence property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getEvidence().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List<Integer> getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList<Integer>();
+    /**
+     * Gets the value of the evidence property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the evidence property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getEvidence().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link Integer }
+     * 
+     * 
+     */
+    public List<Integer> getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList<Integer>();
+        }
+        return this.evidence;
     }
-    return this.evidence;
-  }
 
-  /**
-   * Gets the value of the status property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getStatus()
-  {
-    return status;
-  }
+    /**
+     * Gets the value of the status property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getStatus() {
+        return status;
+    }
 
-  /**
-   * Sets the value of the status property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setStatus(String value)
-  {
-    this.status = value;
-  }
+    /**
+     * Sets the value of the status property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setStatus(String value) {
+        this.status = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/FeatureType.java b/src/jalview/xml/binding/uniprot/FeatureType.java
index fe9f4c4..0a6f7fe 100644
--- a/src/jalview/xml/binding/uniprot/FeatureType.java
+++ b/src/jalview/xml/binding/uniprot/FeatureType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,16 +16,14 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes different types of sequence annotations. Equivalent to the flat
- * file FT-line.
+ * Describes different types of sequence annotations.
+ *             Equivalent to the flat file FT-line.
  * 
- * <p>
- * Java class for featureType complex type.
+ * <p>Java class for featureType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="featureType">
@@ -101,259 +100,254 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "featureType",
-  propOrder =
-  { "original", "variation", "location" })
-public class FeatureType
-{
-
-  protected String original;
-
-  protected List<String> variation;
-
-  @XmlElement(required = true)
-  protected LocationType location;
-
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
+@XmlType(name = "featureType", propOrder = {
+    "original",
+    "variation",
+    "location"
+})
+public class FeatureType {
 
-  @XmlAttribute(name = "status")
-  protected String status;
+    protected String original;
+    protected List<String> variation;
+    @XmlElement(required = true)
+    protected LocationType location;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
+    @XmlAttribute(name = "status")
+    protected String status;
+    @XmlAttribute(name = "id")
+    protected String id;
+    @XmlAttribute(name = "description")
+    protected String description;
+    @XmlAttribute(name = "evidence")
+    protected List<Integer> evidence;
+    @XmlAttribute(name = "ref")
+    protected String ref;
 
-  @XmlAttribute(name = "id")
-  protected String id;
-
-  @XmlAttribute(name = "description")
-  protected String description;
-
-  @XmlAttribute(name = "evidence")
-  protected List<Integer> evidence;
-
-  @XmlAttribute(name = "ref")
-  protected String ref;
-
-  /**
-   * Gets the value of the original property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getOriginal()
-  {
-    return original;
-  }
+    /**
+     * Gets the value of the original property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getOriginal() {
+        return original;
+    }
 
-  /**
-   * Sets the value of the original property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setOriginal(String value)
-  {
-    this.original = value;
-  }
+    /**
+     * Sets the value of the original property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setOriginal(String value) {
+        this.original = value;
+    }
 
-  /**
-   * Gets the value of the variation property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the variation property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getVariation().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link String }
-   * 
-   * 
-   */
-  public List<String> getVariation()
-  {
-    if (variation == null)
-    {
-      variation = new ArrayList<String>();
+    /**
+     * Gets the value of the variation property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the variation property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getVariation().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
+     * 
+     */
+    public List<String> getVariation() {
+        if (variation == null) {
+            variation = new ArrayList<String>();
+        }
+        return this.variation;
     }
-    return this.variation;
-  }
 
-  /**
-   * Gets the value of the location property.
-   * 
-   * @return possible object is {@link LocationType }
-   * 
-   */
-  public LocationType getLocation()
-  {
-    return location;
-  }
+    /**
+     * Gets the value of the location property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link LocationType }
+     *     
+     */
+    public LocationType getLocation() {
+        return location;
+    }
 
-  /**
-   * Sets the value of the location property.
-   * 
-   * @param value
-   *          allowed object is {@link LocationType }
-   * 
-   */
-  public void setLocation(LocationType value)
-  {
-    this.location = value;
-  }
+    /**
+     * Sets the value of the location property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link LocationType }
+     *     
+     */
+    public void setLocation(LocationType value) {
+        this.location = value;
+    }
 
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
+    /**
+     * Gets the value of the type property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getType() {
+        return type;
+    }
 
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
+    /**
+     * Sets the value of the type property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
 
-  /**
-   * Gets the value of the status property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getStatus()
-  {
-    return status;
-  }
+    /**
+     * Gets the value of the status property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getStatus() {
+        return status;
+    }
 
-  /**
-   * Sets the value of the status property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setStatus(String value)
-  {
-    this.status = value;
-  }
+    /**
+     * Sets the value of the status property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setStatus(String value) {
+        this.status = value;
+    }
 
-  /**
-   * Gets the value of the id property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getId()
-  {
-    return id;
-  }
+    /**
+     * Gets the value of the id property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getId() {
+        return id;
+    }
 
-  /**
-   * Sets the value of the id property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setId(String value)
-  {
-    this.id = value;
-  }
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setId(String value) {
+        this.id = value;
+    }
 
-  /**
-   * Gets the value of the description property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDescription()
-  {
-    return description;
-  }
+    /**
+     * Gets the value of the description property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDescription() {
+        return description;
+    }
 
-  /**
-   * Sets the value of the description property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDescription(String value)
-  {
-    this.description = value;
-  }
+    /**
+     * Sets the value of the description property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDescription(String value) {
+        this.description = value;
+    }
 
-  /**
-   * Gets the value of the evidence property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the evidence property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getEvidence().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List<Integer> getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList<Integer>();
+    /**
+     * Gets the value of the evidence property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the evidence property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getEvidence().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link Integer }
+     * 
+     * 
+     */
+    public List<Integer> getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList<Integer>();
+        }
+        return this.evidence;
     }
-    return this.evidence;
-  }
 
-  /**
-   * Gets the value of the ref property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getRef()
-  {
-    return ref;
-  }
+    /**
+     * Gets the value of the ref property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getRef() {
+        return ref;
+    }
 
-  /**
-   * Sets the value of the ref property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setRef(String value)
-  {
-    this.ref = value;
-  }
+    /**
+     * Sets the value of the ref property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setRef(String value) {
+        this.ref = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/GeneLocationType.java b/src/jalview/xml/binding/uniprot/GeneLocationType.java
index 33f0bfd..9a04acc 100644
--- a/src/jalview/xml/binding/uniprot/GeneLocationType.java
+++ b/src/jalview/xml/binding/uniprot/GeneLocationType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -14,16 +15,14 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes non-nuclear gene locations (organelles and plasmids). Equivalent to
- * the flat file OG-line.
+ * Describes non-nuclear gene locations (organelles and plasmids).
+ *             Equivalent to the flat file OG-line.
  * 
- * <p>
- * Java class for geneLocationType complex type.
+ * <p>Java class for geneLocationType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="geneLocationType">
@@ -57,102 +56,97 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "geneLocationType", propOrder = { "name" })
-public class GeneLocationType
-{
-
-  protected List<StatusType> name;
+@XmlType(name = "geneLocationType", propOrder = {
+    "name"
+})
+public class GeneLocationType {
 
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
+    protected List<StatusType> name;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
+    @XmlAttribute(name = "evidence")
+    protected List<Integer> evidence;
 
-  @XmlAttribute(name = "evidence")
-  protected List<Integer> evidence;
-
-  /**
-   * Gets the value of the name property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the name property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getName().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link StatusType
-   * }
-   * 
-   * 
-   */
-  public List<StatusType> getName()
-  {
-    if (name == null)
-    {
-      name = new ArrayList<StatusType>();
+    /**
+     * Gets the value of the name property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the name property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getName().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link StatusType }
+     * 
+     * 
+     */
+    public List<StatusType> getName() {
+        if (name == null) {
+            name = new ArrayList<StatusType>();
+        }
+        return this.name;
     }
-    return this.name;
-  }
 
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
+    /**
+     * Gets the value of the type property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getType() {
+        return type;
+    }
 
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
+    /**
+     * Sets the value of the type property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
 
-  /**
-   * Gets the value of the evidence property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the evidence property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getEvidence().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List<Integer> getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList<Integer>();
+    /**
+     * Gets the value of the evidence property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the evidence property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getEvidence().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link Integer }
+     * 
+     * 
+     */
+    public List<Integer> getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList<Integer>();
+        }
+        return this.evidence;
     }
-    return this.evidence;
-  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/GeneNameType.java b/src/jalview/xml/binding/uniprot/GeneNameType.java
index 84850d3..8b69d3d 100644
--- a/src/jalview/xml/binding/uniprot/GeneNameType.java
+++ b/src/jalview/xml/binding/uniprot/GeneNameType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,16 +16,14 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
+
 /**
- * Describes different types of gene designations. Equivalent to the flat file
- * GN-line.
+ * Describes different types of gene designations.
+ *             Equivalent to the flat file GN-line.
  * 
- * <p>
- * Java class for geneNameType complex type.
+ * <p>Java class for geneNameType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="geneNameType">
@@ -49,94 +48,93 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "geneNameType", propOrder = { "value" })
-public class GeneNameType
-{
-
-  @XmlValue
-  protected String value;
-
-  @XmlAttribute(name = "evidence")
-  protected List<Integer> evidence;
+@XmlType(name = "geneNameType", propOrder = {
+    "value"
+})
+public class GeneNameType {
 
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
+    @XmlValue
+    protected String value;
+    @XmlAttribute(name = "evidence")
+    protected List<Integer> evidence;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
 
-  /**
-   * Gets the value of the value property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getValue()
-  {
-    return value;
-  }
+    /**
+     * Gets the value of the value property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getValue() {
+        return value;
+    }
 
-  /**
-   * Sets the value of the value property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setValue(String value)
-  {
-    this.value = value;
-  }
+    /**
+     * Sets the value of the value property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setValue(String value) {
+        this.value = value;
+    }
 
-  /**
-   * Gets the value of the evidence property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the evidence property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getEvidence().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List<Integer> getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList<Integer>();
+    /**
+     * Gets the value of the evidence property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the evidence property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getEvidence().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link Integer }
+     * 
+     * 
+     */
+    public List<Integer> getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList<Integer>();
+        }
+        return this.evidence;
     }
-    return this.evidence;
-  }
 
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
+    /**
+     * Gets the value of the type property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getType() {
+        return type;
+    }
 
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
+    /**
+     * Sets the value of the type property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/GeneType.java b/src/jalview/xml/binding/uniprot/GeneType.java
index 0b0a19e..24285cb 100644
--- a/src/jalview/xml/binding/uniprot/GeneType.java
+++ b/src/jalview/xml/binding/uniprot/GeneType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -14,15 +15,14 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes a gene. Equivalent to the flat file GN-line.
+ * Describes a gene.
+ *             Equivalent to the flat file GN-line.
  * 
- * <p>
- * Java class for geneType complex type.
+ * <p>Java class for geneType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="geneType">
@@ -39,43 +39,41 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "geneType", propOrder = { "name" })
-public class GeneType
-{
+@XmlType(name = "geneType", propOrder = {
+    "name"
+})
+public class GeneType {
 
-  @XmlElement(required = true)
-  protected List<GeneNameType> name;
+    @XmlElement(required = true)
+    protected List<GeneNameType> name;
 
-  /**
-   * Gets the value of the name property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the name property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getName().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link GeneNameType }
-   * 
-   * 
-   */
-  public List<GeneNameType> getName()
-  {
-    if (name == null)
-    {
-      name = new ArrayList<GeneNameType>();
+    /**
+     * Gets the value of the name property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the name property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getName().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link GeneNameType }
+     * 
+     * 
+     */
+    public List<GeneNameType> getName() {
+        if (name == null) {
+            name = new ArrayList<GeneNameType>();
+        }
+        return this.name;
     }
-    return this.name;
-  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/ImportedFromType.java b/src/jalview/xml/binding/uniprot/ImportedFromType.java
index f46afb5..070e48e 100644
--- a/src/jalview/xml/binding/uniprot/ImportedFromType.java
+++ b/src/jalview/xml/binding/uniprot/ImportedFromType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,16 +13,13 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes the source of the evidence, when it is not assigned by UniProt, but
- * imported from an external database.
+ * Describes the source of the evidence, when it is not assigned by UniProt, but imported from an external database.
  * 
- * <p>
- * Java class for importedFromType complex type.
+ * <p>Java class for importedFromType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="importedFromType">
@@ -38,34 +36,36 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "importedFromType", propOrder = { "dbReference" })
-public class ImportedFromType
-{
+@XmlType(name = "importedFromType", propOrder = {
+    "dbReference"
+})
+public class ImportedFromType {
 
-  @XmlElement(required = true)
-  protected DbReferenceType dbReference;
+    @XmlElement(required = true)
+    protected DbReferenceType dbReference;
 
-  /**
-   * Gets the value of the dbReference property.
-   * 
-   * @return possible object is {@link DbReferenceType }
-   * 
-   */
-  public DbReferenceType getDbReference()
-  {
-    return dbReference;
-  }
+    /**
+     * Gets the value of the dbReference property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link DbReferenceType }
+     *     
+     */
+    public DbReferenceType getDbReference() {
+        return dbReference;
+    }
 
-  /**
-   * Sets the value of the dbReference property.
-   * 
-   * @param value
-   *          allowed object is {@link DbReferenceType }
-   * 
-   */
-  public void setDbReference(DbReferenceType value)
-  {
-    this.dbReference = value;
-  }
+    /**
+     * Sets the value of the dbReference property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link DbReferenceType }
+     *     
+     */
+    public void setDbReference(DbReferenceType value) {
+        this.dbReference = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/InteractantType.java b/src/jalview/xml/binding/uniprot/InteractantType.java
index 0e59c4b..9a0e97a 100644
--- a/src/jalview/xml/binding/uniprot/InteractantType.java
+++ b/src/jalview/xml/binding/uniprot/InteractantType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,13 +13,11 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>
- * Java class for interactantType complex type.
+ * <p>Java class for interactantType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="interactantType">
@@ -34,84 +33,87 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "interactantType", propOrder = { "id", "label" })
-public class InteractantType
-{
-
-  protected String id;
-
-  protected String label;
+@XmlType(name = "interactantType", propOrder = {
+    "id",
+    "label"
+})
+public class InteractantType {
 
-  @XmlAttribute(name = "intactId", required = true)
-  protected String intactId;
+    protected String id;
+    protected String label;
+    @XmlAttribute(name = "intactId", required = true)
+    protected String intactId;
 
-  /**
-   * Gets the value of the id property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getId()
-  {
-    return id;
-  }
+    /**
+     * Gets the value of the id property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getId() {
+        return id;
+    }
 
-  /**
-   * Sets the value of the id property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setId(String value)
-  {
-    this.id = value;
-  }
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setId(String value) {
+        this.id = value;
+    }
 
-  /**
-   * Gets the value of the label property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getLabel()
-  {
-    return label;
-  }
+    /**
+     * Gets the value of the label property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getLabel() {
+        return label;
+    }
 
-  /**
-   * Sets the value of the label property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setLabel(String value)
-  {
-    this.label = value;
-  }
+    /**
+     * Sets the value of the label property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setLabel(String value) {
+        this.label = value;
+    }
 
-  /**
-   * Gets the value of the intactId property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getIntactId()
-  {
-    return intactId;
-  }
+    /**
+     * Gets the value of the intactId property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getIntactId() {
+        return intactId;
+    }
 
-  /**
-   * Sets the value of the intactId property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setIntactId(String value)
-  {
-    this.intactId = value;
-  }
+    /**
+     * Sets the value of the intactId property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setIntactId(String value) {
+        this.intactId = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/IsoformType.java b/src/jalview/xml/binding/uniprot/IsoformType.java
index 631ab01..33710ef 100644
--- a/src/jalview/xml/binding/uniprot/IsoformType.java
+++ b/src/jalview/xml/binding/uniprot/IsoformType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -16,15 +17,13 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
+
 /**
  * Describes isoforms in 'alternative products' annotations.
  * 
- * <p>
- * Java class for isoformType complex type.
+ * <p>Java class for isoformType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="isoformType">
@@ -70,316 +69,302 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "isoformType",
-  propOrder =
-  { "id", "name", "sequence", "text" })
-public class IsoformType
-{
-
-  @XmlElement(required = true)
-  protected List<String> id;
-
-  @XmlElement(required = true)
-  protected List<IsoformType.Name> name;
-
-  @XmlElement(required = true)
-  protected IsoformType.Sequence sequence;
-
-  protected List<EvidencedStringType> text;
-
-  /**
-   * Gets the value of the id property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the id property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getId().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link String }
-   * 
-   * 
-   */
-  public List<String> getId()
-  {
-    if (id == null)
-    {
-      id = new ArrayList<String>();
-    }
-    return this.id;
-  }
-
-  /**
-   * Gets the value of the name property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the name property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getName().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link IsoformType.Name }
-   * 
-   * 
-   */
-  public List<IsoformType.Name> getName()
-  {
-    if (name == null)
-    {
-      name = new ArrayList<IsoformType.Name>();
-    }
-    return this.name;
-  }
+@XmlType(name = "isoformType", propOrder = {
+    "id",
+    "name",
+    "sequence",
+    "text"
+})
+public class IsoformType {
 
-  /**
-   * Gets the value of the sequence property.
-   * 
-   * @return possible object is {@link IsoformType.Sequence }
-   * 
-   */
-  public IsoformType.Sequence getSequence()
-  {
-    return sequence;
-  }
-
-  /**
-   * Sets the value of the sequence property.
-   * 
-   * @param value
-   *          allowed object is {@link IsoformType.Sequence }
-   * 
-   */
-  public void setSequence(IsoformType.Sequence value)
-  {
-    this.sequence = value;
-  }
-
-  /**
-   * Gets the value of the text property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the text property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getText().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link EvidencedStringType }
-   * 
-   * 
-   */
-  public List<EvidencedStringType> getText()
-  {
-    if (text == null)
-    {
-      text = new ArrayList<EvidencedStringType>();
-    }
-    return this.text;
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;simpleContent>
-   *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
-   *       &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-   *     &lt;/extension>
-   *   &lt;/simpleContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "value" })
-  public static class Name
-  {
-
-    @XmlValue
-    protected String value;
-
-    @XmlAttribute(name = "evidence")
-    protected List<Integer> evidence;
+    @XmlElement(required = true)
+    protected List<String> id;
+    @XmlElement(required = true)
+    protected List<IsoformType.Name> name;
+    @XmlElement(required = true)
+    protected IsoformType.Sequence sequence;
+    protected List<EvidencedStringType> text;
 
     /**
-     * Gets the value of the value property.
+     * Gets the value of the id property.
      * 
-     * @return possible object is {@link String }
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the id property.
      * 
-     */
-    public String getValue()
-    {
-      return value;
-    }
-
-    /**
-     * Sets the value of the value property.
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getId().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
      * 
-     * @param value
-     *          allowed object is {@link String }
      * 
      */
-    public void setValue(String value)
-    {
-      this.value = value;
+    public List<String> getId() {
+        if (id == null) {
+            id = new ArrayList<String>();
+        }
+        return this.id;
     }
 
     /**
-     * Gets the value of the evidence property.
+     * Gets the value of the name property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the evidence property.
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the name property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
-     * 
      * <pre>
-     * getEvidence().add(newItem);
+     *    getName().add(newItem);
      * </pre>
      * 
      * 
      * <p>
-     * Objects of the following type(s) are allowed in the list {@link Integer }
+     * Objects of the following type(s) are allowed in the list
+     * {@link IsoformType.Name }
      * 
      * 
      */
-    public List<Integer> getEvidence()
-    {
-      if (evidence == null)
-      {
-        evidence = new ArrayList<Integer>();
-      }
-      return this.evidence;
+    public List<IsoformType.Name> getName() {
+        if (name == null) {
+            name = new ArrayList<IsoformType.Name>();
+        }
+        return this.name;
     }
 
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;attribute name="type" use="required">
-   *         &lt;simpleType>
-   *           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
-   *             &lt;enumeration value="not described"/>
-   *             &lt;enumeration value="described"/>
-   *             &lt;enumeration value="displayed"/>
-   *             &lt;enumeration value="external"/>
-   *           &lt;/restriction>
-   *         &lt;/simpleType>
-   *       &lt;/attribute>
-   *       &lt;attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class Sequence
-  {
-
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-
-    @XmlAttribute(name = "ref")
-    protected String ref;
-
     /**
-     * Gets the value of the type property.
-     * 
-     * @return possible object is {@link String }
+     * Gets the value of the sequence property.
      * 
+     * @return
+     *     possible object is
+     *     {@link IsoformType.Sequence }
+     *     
      */
-    public String getType()
-    {
-      return type;
+    public IsoformType.Sequence getSequence() {
+        return sequence;
     }
 
     /**
-     * Sets the value of the type property.
+     * Sets the value of the sequence property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link IsoformType.Sequence }
+     *     
      */
-    public void setType(String value)
-    {
-      this.type = value;
+    public void setSequence(IsoformType.Sequence value) {
+        this.sequence = value;
     }
 
     /**
-     * Gets the value of the ref property.
+     * Gets the value of the text property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the text property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getText().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link EvidencedStringType }
      * 
-     * @return possible object is {@link String }
      * 
      */
-    public String getRef()
-    {
-      return ref;
+    public List<EvidencedStringType> getText() {
+        if (text == null) {
+            text = new ArrayList<EvidencedStringType>();
+        }
+        return this.text;
     }
 
+
     /**
-     * Sets the value of the ref property.
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;simpleContent>
+     *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
+     *       &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+     *     &lt;/extension>
+     *   &lt;/simpleContent>
+     * &lt;/complexType>
+     * </pre>
      * 
-     * @param value
-     *          allowed object is {@link String }
      * 
      */
-    public void setRef(String value)
-    {
-      this.ref = value;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "value"
+    })
+    public static class Name {
+
+        @XmlValue
+        protected String value;
+        @XmlAttribute(name = "evidence")
+        protected List<Integer> evidence;
+
+        /**
+         * Gets the value of the value property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getValue() {
+            return value;
+        }
+
+        /**
+         * Sets the value of the value property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setValue(String value) {
+            this.value = value;
+        }
+
+        /**
+         * Gets the value of the evidence property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the evidence property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getEvidence().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link Integer }
+         * 
+         * 
+         */
+        public List<Integer> getEvidence() {
+            if (evidence == null) {
+                evidence = new ArrayList<Integer>();
+            }
+            return this.evidence;
+        }
+
     }
 
-  }
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attribute name="type" use="required">
+     *         &lt;simpleType>
+     *           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
+     *             &lt;enumeration value="not described"/>
+     *             &lt;enumeration value="described"/>
+     *             &lt;enumeration value="displayed"/>
+     *             &lt;enumeration value="external"/>
+     *           &lt;/restriction>
+     *         &lt;/simpleType>
+     *       &lt;/attribute>
+     *       &lt;attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class Sequence {
+
+        @XmlAttribute(name = "type", required = true)
+        protected String type;
+        @XmlAttribute(name = "ref")
+        protected String ref;
+
+        /**
+         * Gets the value of the type property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getType() {
+            return type;
+        }
+
+        /**
+         * Sets the value of the type property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setType(String value) {
+            this.type = value;
+        }
+
+        /**
+         * Gets the value of the ref property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getRef() {
+            return ref;
+        }
+
+        /**
+         * Sets the value of the ref property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setRef(String value) {
+            this.ref = value;
+        }
+
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/KeywordType.java b/src/jalview/xml/binding/uniprot/KeywordType.java
index ac58dfd..3f1a75f 100644
--- a/src/jalview/xml/binding/uniprot/KeywordType.java
+++ b/src/jalview/xml/binding/uniprot/KeywordType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,13 +16,11 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
+
 /**
- * <p>
- * Java class for keywordType complex type.
+ * <p>Java class for keywordType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="keywordType">
@@ -37,94 +36,93 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "keywordType", propOrder = { "value" })
-public class KeywordType
-{
-
-  @XmlValue
-  protected String value;
-
-  @XmlAttribute(name = "evidence")
-  protected List<Integer> evidence;
+@XmlType(name = "keywordType", propOrder = {
+    "value"
+})
+public class KeywordType {
 
-  @XmlAttribute(name = "id", required = true)
-  protected String id;
+    @XmlValue
+    protected String value;
+    @XmlAttribute(name = "evidence")
+    protected List<Integer> evidence;
+    @XmlAttribute(name = "id", required = true)
+    protected String id;
 
-  /**
-   * Gets the value of the value property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getValue()
-  {
-    return value;
-  }
+    /**
+     * Gets the value of the value property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getValue() {
+        return value;
+    }
 
-  /**
-   * Sets the value of the value property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setValue(String value)
-  {
-    this.value = value;
-  }
+    /**
+     * Sets the value of the value property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setValue(String value) {
+        this.value = value;
+    }
 
-  /**
-   * Gets the value of the evidence property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the evidence property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getEvidence().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List<Integer> getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList<Integer>();
+    /**
+     * Gets the value of the evidence property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the evidence property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getEvidence().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link Integer }
+     * 
+     * 
+     */
+    public List<Integer> getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList<Integer>();
+        }
+        return this.evidence;
     }
-    return this.evidence;
-  }
 
-  /**
-   * Gets the value of the id property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getId()
-  {
-    return id;
-  }
+    /**
+     * Gets the value of the id property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getId() {
+        return id;
+    }
 
-  /**
-   * Sets the value of the id property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setId(String value)
-  {
-    this.id = value;
-  }
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setId(String value) {
+        this.id = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/LocationType.java b/src/jalview/xml/binding/uniprot/LocationType.java
index d1d1457..5d7e7e9 100644
--- a/src/jalview/xml/binding/uniprot/LocationType.java
+++ b/src/jalview/xml/binding/uniprot/LocationType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,17 +13,13 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes a sequence location as either a range with a begin and end or as a
- * position. The 'sequence' attribute is only used when the location is not on
- * the canonical sequence displayed in the current entry.
+ * Describes a sequence location as either a range with a begin and end or as a position. The 'sequence' attribute is only used when the location is not on the canonical sequence displayed in the current entry.
  * 
- * <p>
- * Java class for locationType complex type.
+ * <p>Java class for locationType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="locationType">
@@ -44,109 +41,113 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "locationType", propOrder = { "begin", "end", "position" })
-public class LocationType
-{
-
-  protected PositionType begin;
-
-  protected PositionType end;
-
-  protected PositionType position;
-
-  @XmlAttribute(name = "sequence")
-  protected String sequence;
-
-  /**
-   * Gets the value of the begin property.
-   * 
-   * @return possible object is {@link PositionType }
-   * 
-   */
-  public PositionType getBegin()
-  {
-    return begin;
-  }
-
-  /**
-   * Sets the value of the begin property.
-   * 
-   * @param value
-   *          allowed object is {@link PositionType }
-   * 
-   */
-  public void setBegin(PositionType value)
-  {
-    this.begin = value;
-  }
-
-  /**
-   * Gets the value of the end property.
-   * 
-   * @return possible object is {@link PositionType }
-   * 
-   */
-  public PositionType getEnd()
-  {
-    return end;
-  }
-
-  /**
-   * Sets the value of the end property.
-   * 
-   * @param value
-   *          allowed object is {@link PositionType }
-   * 
-   */
-  public void setEnd(PositionType value)
-  {
-    this.end = value;
-  }
-
-  /**
-   * Gets the value of the position property.
-   * 
-   * @return possible object is {@link PositionType }
-   * 
-   */
-  public PositionType getPosition()
-  {
-    return position;
-  }
-
-  /**
-   * Sets the value of the position property.
-   * 
-   * @param value
-   *          allowed object is {@link PositionType }
-   * 
-   */
-  public void setPosition(PositionType value)
-  {
-    this.position = value;
-  }
-
-  /**
-   * Gets the value of the sequence property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getSequence()
-  {
-    return sequence;
-  }
-
-  /**
-   * Sets the value of the sequence property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setSequence(String value)
-  {
-    this.sequence = value;
-  }
+@XmlType(name = "locationType", propOrder = {
+    "begin",
+    "end",
+    "position"
+})
+public class LocationType {
+
+    protected PositionType begin;
+    protected PositionType end;
+    protected PositionType position;
+    @XmlAttribute(name = "sequence")
+    protected String sequence;
+
+    /**
+     * Gets the value of the begin property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link PositionType }
+     *     
+     */
+    public PositionType getBegin() {
+        return begin;
+    }
+
+    /**
+     * Sets the value of the begin property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link PositionType }
+     *     
+     */
+    public void setBegin(PositionType value) {
+        this.begin = value;
+    }
+
+    /**
+     * Gets the value of the end property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link PositionType }
+     *     
+     */
+    public PositionType getEnd() {
+        return end;
+    }
+
+    /**
+     * Sets the value of the end property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link PositionType }
+     *     
+     */
+    public void setEnd(PositionType value) {
+        this.end = value;
+    }
+
+    /**
+     * Gets the value of the position property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link PositionType }
+     *     
+     */
+    public PositionType getPosition() {
+        return position;
+    }
+
+    /**
+     * Sets the value of the position property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link PositionType }
+     *     
+     */
+    public void setPosition(PositionType value) {
+        this.position = value;
+    }
+
+    /**
+     * Gets the value of the sequence property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getSequence() {
+        return sequence;
+    }
+
+    /**
+     * Sets the value of the sequence property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setSequence(String value) {
+        this.sequence = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/MoleculeType.java b/src/jalview/xml/binding/uniprot/MoleculeType.java
index 72f6c4f..b7657f8 100644
--- a/src/jalview/xml/binding/uniprot/MoleculeType.java
+++ b/src/jalview/xml/binding/uniprot/MoleculeType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,15 +14,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
+
 /**
  * Describes a molecule by name or unique identifier.
  * 
- * <p>
- * Java class for moleculeType complex type.
+ * <p>Java class for moleculeType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="moleculeType">
@@ -36,60 +35,62 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "moleculeType", propOrder = { "value" })
-public class MoleculeType
-{
-
-  @XmlValue
-  protected String value;
+@XmlType(name = "moleculeType", propOrder = {
+    "value"
+})
+public class MoleculeType {
 
-  @XmlAttribute(name = "id")
-  protected String id;
+    @XmlValue
+    protected String value;
+    @XmlAttribute(name = "id")
+    protected String id;
 
-  /**
-   * Gets the value of the value property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getValue()
-  {
-    return value;
-  }
+    /**
+     * Gets the value of the value property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getValue() {
+        return value;
+    }
 
-  /**
-   * Sets the value of the value property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setValue(String value)
-  {
-    this.value = value;
-  }
+    /**
+     * Sets the value of the value property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setValue(String value) {
+        this.value = value;
+    }
 
-  /**
-   * Gets the value of the id property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getId()
-  {
-    return id;
-  }
+    /**
+     * Gets the value of the id property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getId() {
+        return id;
+    }
 
-  /**
-   * Sets the value of the id property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setId(String value)
-  {
-    this.id = value;
-  }
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setId(String value) {
+        this.id = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/NameListType.java b/src/jalview/xml/binding/uniprot/NameListType.java
index 947f2f4..c316941 100644
--- a/src/jalview/xml/binding/uniprot/NameListType.java
+++ b/src/jalview/xml/binding/uniprot/NameListType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,13 +16,11 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlElements;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>
- * Java class for nameListType complex type.
+ * <p>Java class for nameListType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="nameListType">
@@ -39,45 +38,45 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "nameListType", propOrder = { "consortiumOrPerson" })
-public class NameListType
-{
+@XmlType(name = "nameListType", propOrder = {
+    "consortiumOrPerson"
+})
+public class NameListType {
 
-  @XmlElements({
-      @XmlElement(name = "consortium", type = ConsortiumType.class),
-      @XmlElement(name = "person", type = PersonType.class) })
-  protected List<Object> consortiumOrPerson;
+    @XmlElements({
+        @XmlElement(name = "consortium", type = ConsortiumType.class),
+        @XmlElement(name = "person", type = PersonType.class)
+    })
+    protected List<Object> consortiumOrPerson;
 
-  /**
-   * Gets the value of the consortiumOrPerson property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the consortiumOrPerson property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getConsortiumOrPerson().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link ConsortiumType } {@link PersonType }
-   * 
-   * 
-   */
-  public List<Object> getConsortiumOrPerson()
-  {
-    if (consortiumOrPerson == null)
-    {
-      consortiumOrPerson = new ArrayList<Object>();
+    /**
+     * Gets the value of the consortiumOrPerson property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the consortiumOrPerson property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getConsortiumOrPerson().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link ConsortiumType }
+     * {@link PersonType }
+     * 
+     * 
+     */
+    public List<Object> getConsortiumOrPerson() {
+        if (consortiumOrPerson == null) {
+            consortiumOrPerson = new ArrayList<Object>();
+        }
+        return this.consortiumOrPerson;
     }
-    return this.consortiumOrPerson;
-  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/ObjectFactory.java b/src/jalview/xml/binding/uniprot/ObjectFactory.java
index a647bd0..324ef9f 100644
--- a/src/jalview/xml/binding/uniprot/ObjectFactory.java
+++ b/src/jalview/xml/binding/uniprot/ObjectFactory.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.JAXBElement;
@@ -12,558 +13,496 @@ import javax.xml.bind.annotation.XmlElementDecl;
 import javax.xml.bind.annotation.XmlRegistry;
 import javax.xml.namespace.QName;
 
+
 /**
- * This object contains factory methods for each Java content interface and Java
- * element interface generated in the jalview.xml.binding.uniprot package.
- * <p>
- * An ObjectFactory allows you to programatically construct new instances of the
- * Java representation for XML content. The Java representation of XML content
- * can consist of schema derived interfaces and classes representing the binding
- * of schema type definitions, element declarations and model groups. Factory
- * methods for each of these are provided in this class.
+ * This object contains factory methods for each 
+ * Java content interface and Java element interface 
+ * generated in the jalview.xml.binding.uniprot package. 
+ * <p>An ObjectFactory allows you to programatically 
+ * construct new instances of the Java representation 
+ * for XML content. The Java representation of XML 
+ * content can consist of schema derived interfaces 
+ * and classes representing the binding of schema 
+ * type definitions, element declarations and model 
+ * groups.  Factory methods for each of these are 
+ * provided in this class.
  * 
  */
 @XmlRegistry
-public class ObjectFactory
-{
-
-  private final static QName _Copyright_QNAME = new QName(
-          "http://uniprot.org/uniprot", "copyright");
-
-  /**
-   * Create a new ObjectFactory that can be used to create new instances of
-   * schema derived classes for package: jalview.xml.binding.uniprot
-   * 
-   */
-  public ObjectFactory()
-  {
-  }
-
-  /**
-   * Create an instance of {@link SourceDataType }
-   * 
-   */
-  public SourceDataType createSourceDataType()
-  {
-    return new SourceDataType();
-  }
-
-  /**
-   * Create an instance of {@link IsoformType }
-   * 
-   */
-  public IsoformType createIsoformType()
-  {
-    return new IsoformType();
-  }
-
-  /**
-   * Create an instance of {@link CommentType }
-   * 
-   */
-  public CommentType createCommentType()
-  {
-    return new CommentType();
-  }
-
-  /**
-   * Create an instance of {@link CommentType.Conflict }
-   * 
-   */
-  public CommentType.Conflict createCommentTypeConflict()
-  {
-    return new CommentType.Conflict();
-  }
-
-  /**
-   * Create an instance of {@link OrganismType }
-   * 
-   */
-  public OrganismType createOrganismType()
-  {
-    return new OrganismType();
-  }
-
-  /**
-   * Create an instance of {@link ProteinType }
-   * 
-   */
-  public ProteinType createProteinType()
-  {
-    return new ProteinType();
-  }
-
-  /**
-   * Create an instance of {@link Entry }
-   * 
-   */
-  public Entry createEntry()
-  {
-    return new Entry();
-  }
-
-  /**
-   * Create an instance of {@link GeneType }
-   * 
-   */
-  public GeneType createGeneType()
-  {
-    return new GeneType();
-  }
-
-  /**
-   * Create an instance of {@link GeneLocationType }
-   * 
-   */
-  public GeneLocationType createGeneLocationType()
-  {
-    return new GeneLocationType();
-  }
-
-  /**
-   * Create an instance of {@link ReferenceType }
-   * 
-   */
-  public ReferenceType createReferenceType()
-  {
-    return new ReferenceType();
-  }
-
-  /**
-   * Create an instance of {@link DbReferenceType }
-   * 
-   */
-  public DbReferenceType createDbReferenceType()
-  {
-    return new DbReferenceType();
-  }
-
-  /**
-   * Create an instance of {@link ProteinExistenceType }
-   * 
-   */
-  public ProteinExistenceType createProteinExistenceType()
-  {
-    return new ProteinExistenceType();
-  }
-
-  /**
-   * Create an instance of {@link KeywordType }
-   * 
-   */
-  public KeywordType createKeywordType()
-  {
-    return new KeywordType();
-  }
-
-  /**
-   * Create an instance of {@link FeatureType }
-   * 
-   */
-  public FeatureType createFeatureType()
-  {
-    return new FeatureType();
-  }
-
-  /**
-   * Create an instance of {@link EvidenceType }
-   * 
-   */
-  public EvidenceType createEvidenceType()
-  {
-    return new EvidenceType();
-  }
-
-  /**
-   * Create an instance of {@link SequenceType }
-   * 
-   */
-  public SequenceType createSequenceType()
-  {
-    return new SequenceType();
-  }
-
-  /**
-   * Create an instance of {@link Uniprot }
-   * 
-   */
-  public Uniprot createUniprot()
-  {
-    return new Uniprot();
-  }
-
-  /**
-   * Create an instance of {@link StatusType }
-   * 
-   */
-  public StatusType createStatusType()
-  {
-    return new StatusType();
-  }
-
-  /**
-   * Create an instance of {@link PositionType }
-   * 
-   */
-  public PositionType createPositionType()
-  {
-    return new PositionType();
-  }
-
-  /**
-   * Create an instance of {@link ConsortiumType }
-   * 
-   */
-  public ConsortiumType createConsortiumType()
-  {
-    return new ConsortiumType();
-  }
-
-  /**
-   * Create an instance of {@link GeneNameType }
-   * 
-   */
-  public GeneNameType createGeneNameType()
-  {
-    return new GeneNameType();
-  }
-
-  /**
-   * Create an instance of {@link LocationType }
-   * 
-   */
-  public LocationType createLocationType()
-  {
-    return new LocationType();
-  }
-
-  /**
-   * Create an instance of {@link CitationType }
-   * 
-   */
-  public CitationType createCitationType()
-  {
-    return new CitationType();
-  }
-
-  /**
-   * Create an instance of {@link PropertyType }
-   * 
-   */
-  public PropertyType createPropertyType()
-  {
-    return new PropertyType();
-  }
-
-  /**
-   * Create an instance of {@link PhysiologicalReactionType }
-   * 
-   */
-  public PhysiologicalReactionType createPhysiologicalReactionType()
-  {
-    return new PhysiologicalReactionType();
-  }
-
-  /**
-   * Create an instance of {@link CofactorType }
-   * 
-   */
-  public CofactorType createCofactorType()
-  {
-    return new CofactorType();
-  }
-
-  /**
-   * Create an instance of {@link EvidencedStringType }
-   * 
-   */
-  public EvidencedStringType createEvidencedStringType()
-  {
-    return new EvidencedStringType();
-  }
-
-  /**
-   * Create an instance of {@link PersonType }
-   * 
-   */
-  public PersonType createPersonType()
-  {
-    return new PersonType();
-  }
-
-  /**
-   * Create an instance of {@link ImportedFromType }
-   * 
-   */
-  public ImportedFromType createImportedFromType()
-  {
-    return new ImportedFromType();
-  }
-
-  /**
-   * Create an instance of {@link EventType }
-   * 
-   */
-  public EventType createEventType()
-  {
-    return new EventType();
-  }
-
-  /**
-   * Create an instance of {@link InteractantType }
-   * 
-   */
-  public InteractantType createInteractantType()
-  {
-    return new InteractantType();
-  }
-
-  /**
-   * Create an instance of {@link NameListType }
-   * 
-   */
-  public NameListType createNameListType()
-  {
-    return new NameListType();
-  }
-
-  /**
-   * Create an instance of {@link ReactionType }
-   * 
-   */
-  public ReactionType createReactionType()
-  {
-    return new ReactionType();
-  }
-
-  /**
-   * Create an instance of {@link SourceType }
-   * 
-   */
-  public SourceType createSourceType()
-  {
-    return new SourceType();
-  }
-
-  /**
-   * Create an instance of {@link MoleculeType }
-   * 
-   */
-  public MoleculeType createMoleculeType()
-  {
-    return new MoleculeType();
-  }
-
-  /**
-   * Create an instance of {@link OrganismNameType }
-   * 
-   */
-  public OrganismNameType createOrganismNameType()
-  {
-    return new OrganismNameType();
-  }
-
-  /**
-   * Create an instance of {@link SubcellularLocationType }
-   * 
-   */
-  public SubcellularLocationType createSubcellularLocationType()
-  {
-    return new SubcellularLocationType();
-  }
-
-  /**
-   * Create an instance of {@link SourceDataType.Strain }
-   * 
-   */
-  public SourceDataType.Strain createSourceDataTypeStrain()
-  {
-    return new SourceDataType.Strain();
-  }
-
-  /**
-   * Create an instance of {@link SourceDataType.Plasmid }
-   * 
-   */
-  public SourceDataType.Plasmid createSourceDataTypePlasmid()
-  {
-    return new SourceDataType.Plasmid();
-  }
-
-  /**
-   * Create an instance of {@link SourceDataType.Transposon }
-   * 
-   */
-  public SourceDataType.Transposon createSourceDataTypeTransposon()
-  {
-    return new SourceDataType.Transposon();
-  }
-
-  /**
-   * Create an instance of {@link SourceDataType.Tissue }
-   * 
-   */
-  public SourceDataType.Tissue createSourceDataTypeTissue()
-  {
-    return new SourceDataType.Tissue();
-  }
-
-  /**
-   * Create an instance of {@link IsoformType.Name }
-   * 
-   */
-  public IsoformType.Name createIsoformTypeName()
-  {
-    return new IsoformType.Name();
-  }
-
-  /**
-   * Create an instance of {@link IsoformType.Sequence }
-   * 
-   */
-  public IsoformType.Sequence createIsoformTypeSequence()
-  {
-    return new IsoformType.Sequence();
-  }
-
-  /**
-   * Create an instance of {@link CommentType.Absorption }
-   * 
-   */
-  public CommentType.Absorption createCommentTypeAbsorption()
-  {
-    return new CommentType.Absorption();
-  }
-
-  /**
-   * Create an instance of {@link CommentType.Kinetics }
-   * 
-   */
-  public CommentType.Kinetics createCommentTypeKinetics()
-  {
-    return new CommentType.Kinetics();
-  }
-
-  /**
-   * Create an instance of {@link CommentType.PhDependence }
-   * 
-   */
-  public CommentType.PhDependence createCommentTypePhDependence()
-  {
-    return new CommentType.PhDependence();
-  }
-
-  /**
-   * Create an instance of {@link CommentType.RedoxPotential }
-   * 
-   */
-  public CommentType.RedoxPotential createCommentTypeRedoxPotential()
-  {
-    return new CommentType.RedoxPotential();
-  }
-
-  /**
-   * Create an instance of {@link CommentType.TemperatureDependence }
-   * 
-   */
-  public CommentType.TemperatureDependence createCommentTypeTemperatureDependence()
-  {
-    return new CommentType.TemperatureDependence();
-  }
-
-  /**
-   * Create an instance of {@link CommentType.Link }
-   * 
-   */
-  public CommentType.Link createCommentTypeLink()
-  {
-    return new CommentType.Link();
-  }
-
-  /**
-   * Create an instance of {@link CommentType.Disease }
-   * 
-   */
-  public CommentType.Disease createCommentTypeDisease()
-  {
-    return new CommentType.Disease();
-  }
-
-  /**
-   * Create an instance of {@link CommentType.Conflict.Sequence }
-   * 
-   */
-  public CommentType.Conflict.Sequence createCommentTypeConflictSequence()
-  {
-    return new CommentType.Conflict.Sequence();
-  }
-
-  /**
-   * Create an instance of {@link OrganismType.Lineage }
-   * 
-   */
-  public OrganismType.Lineage createOrganismTypeLineage()
-  {
-    return new OrganismType.Lineage();
-  }
-
-  /**
-   * Create an instance of {@link ProteinType.RecommendedName }
-   * 
-   */
-  public ProteinType.RecommendedName createProteinTypeRecommendedName()
-  {
-    return new ProteinType.RecommendedName();
-  }
-
-  /**
-   * Create an instance of {@link ProteinType.AlternativeName }
-   * 
-   */
-  public ProteinType.AlternativeName createProteinTypeAlternativeName()
-  {
-    return new ProteinType.AlternativeName();
-  }
-
-  /**
-   * Create an instance of {@link ProteinType.SubmittedName }
-   * 
-   */
-  public ProteinType.SubmittedName createProteinTypeSubmittedName()
-  {
-    return new ProteinType.SubmittedName();
-  }
-
-  /**
-   * Create an instance of {@link ProteinType.Domain }
-   * 
-   */
-  public ProteinType.Domain createProteinTypeDomain()
-  {
-    return new ProteinType.Domain();
-  }
-
-  /**
-   * Create an instance of {@link ProteinType.Component }
-   * 
-   */
-  public ProteinType.Component createProteinTypeComponent()
-  {
-    return new ProteinType.Component();
-  }
-
-  /**
-   * Create an instance of {@link JAXBElement }{@code <}{@link String
-   * }{@code >}}
-   * 
-   */
-  @XmlElementDecl(
-    namespace = "http://uniprot.org/uniprot",
-    name = "copyright")
-  public JAXBElement<String> createCopyright(String value)
-  {
-    return new JAXBElement<String>(_Copyright_QNAME, String.class, null,
-            value);
-  }
+public class ObjectFactory {
+
+    private final static QName _Copyright_QNAME = new QName("http://uniprot.org/uniprot", "copyright");
+
+    /**
+     * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.uniprot
+     * 
+     */
+    public ObjectFactory() {
+    }
+
+    /**
+     * Create an instance of {@link SourceDataType }
+     * 
+     */
+    public SourceDataType createSourceDataType() {
+        return new SourceDataType();
+    }
+
+    /**
+     * Create an instance of {@link IsoformType }
+     * 
+     */
+    public IsoformType createIsoformType() {
+        return new IsoformType();
+    }
+
+    /**
+     * Create an instance of {@link CommentType }
+     * 
+     */
+    public CommentType createCommentType() {
+        return new CommentType();
+    }
+
+    /**
+     * Create an instance of {@link CommentType.Conflict }
+     * 
+     */
+    public CommentType.Conflict createCommentTypeConflict() {
+        return new CommentType.Conflict();
+    }
+
+    /**
+     * Create an instance of {@link OrganismType }
+     * 
+     */
+    public OrganismType createOrganismType() {
+        return new OrganismType();
+    }
+
+    /**
+     * Create an instance of {@link ProteinType }
+     * 
+     */
+    public ProteinType createProteinType() {
+        return new ProteinType();
+    }
+
+    /**
+     * Create an instance of {@link Entry }
+     * 
+     */
+    public Entry createEntry() {
+        return new Entry();
+    }
+
+    /**
+     * Create an instance of {@link GeneType }
+     * 
+     */
+    public GeneType createGeneType() {
+        return new GeneType();
+    }
+
+    /**
+     * Create an instance of {@link GeneLocationType }
+     * 
+     */
+    public GeneLocationType createGeneLocationType() {
+        return new GeneLocationType();
+    }
+
+    /**
+     * Create an instance of {@link ReferenceType }
+     * 
+     */
+    public ReferenceType createReferenceType() {
+        return new ReferenceType();
+    }
+
+    /**
+     * Create an instance of {@link DbReferenceType }
+     * 
+     */
+    public DbReferenceType createDbReferenceType() {
+        return new DbReferenceType();
+    }
+
+    /**
+     * Create an instance of {@link ProteinExistenceType }
+     * 
+     */
+    public ProteinExistenceType createProteinExistenceType() {
+        return new ProteinExistenceType();
+    }
+
+    /**
+     * Create an instance of {@link KeywordType }
+     * 
+     */
+    public KeywordType createKeywordType() {
+        return new KeywordType();
+    }
+
+    /**
+     * Create an instance of {@link FeatureType }
+     * 
+     */
+    public FeatureType createFeatureType() {
+        return new FeatureType();
+    }
+
+    /**
+     * Create an instance of {@link EvidenceType }
+     * 
+     */
+    public EvidenceType createEvidenceType() {
+        return new EvidenceType();
+    }
+
+    /**
+     * Create an instance of {@link SequenceType }
+     * 
+     */
+    public SequenceType createSequenceType() {
+        return new SequenceType();
+    }
+
+    /**
+     * Create an instance of {@link Uniprot }
+     * 
+     */
+    public Uniprot createUniprot() {
+        return new Uniprot();
+    }
+
+    /**
+     * Create an instance of {@link StatusType }
+     * 
+     */
+    public StatusType createStatusType() {
+        return new StatusType();
+    }
+
+    /**
+     * Create an instance of {@link PositionType }
+     * 
+     */
+    public PositionType createPositionType() {
+        return new PositionType();
+    }
+
+    /**
+     * Create an instance of {@link ConsortiumType }
+     * 
+     */
+    public ConsortiumType createConsortiumType() {
+        return new ConsortiumType();
+    }
+
+    /**
+     * Create an instance of {@link GeneNameType }
+     * 
+     */
+    public GeneNameType createGeneNameType() {
+        return new GeneNameType();
+    }
+
+    /**
+     * Create an instance of {@link LocationType }
+     * 
+     */
+    public LocationType createLocationType() {
+        return new LocationType();
+    }
+
+    /**
+     * Create an instance of {@link CitationType }
+     * 
+     */
+    public CitationType createCitationType() {
+        return new CitationType();
+    }
+
+    /**
+     * Create an instance of {@link PropertyType }
+     * 
+     */
+    public PropertyType createPropertyType() {
+        return new PropertyType();
+    }
+
+    /**
+     * Create an instance of {@link PhysiologicalReactionType }
+     * 
+     */
+    public PhysiologicalReactionType createPhysiologicalReactionType() {
+        return new PhysiologicalReactionType();
+    }
+
+    /**
+     * Create an instance of {@link CofactorType }
+     * 
+     */
+    public CofactorType createCofactorType() {
+        return new CofactorType();
+    }
+
+    /**
+     * Create an instance of {@link EvidencedStringType }
+     * 
+     */
+    public EvidencedStringType createEvidencedStringType() {
+        return new EvidencedStringType();
+    }
+
+    /**
+     * Create an instance of {@link PersonType }
+     * 
+     */
+    public PersonType createPersonType() {
+        return new PersonType();
+    }
+
+    /**
+     * Create an instance of {@link ImportedFromType }
+     * 
+     */
+    public ImportedFromType createImportedFromType() {
+        return new ImportedFromType();
+    }
+
+    /**
+     * Create an instance of {@link EventType }
+     * 
+     */
+    public EventType createEventType() {
+        return new EventType();
+    }
+
+    /**
+     * Create an instance of {@link InteractantType }
+     * 
+     */
+    public InteractantType createInteractantType() {
+        return new InteractantType();
+    }
+
+    /**
+     * Create an instance of {@link NameListType }
+     * 
+     */
+    public NameListType createNameListType() {
+        return new NameListType();
+    }
+
+    /**
+     * Create an instance of {@link ReactionType }
+     * 
+     */
+    public ReactionType createReactionType() {
+        return new ReactionType();
+    }
+
+    /**
+     * Create an instance of {@link SourceType }
+     * 
+     */
+    public SourceType createSourceType() {
+        return new SourceType();
+    }
+
+    /**
+     * Create an instance of {@link MoleculeType }
+     * 
+     */
+    public MoleculeType createMoleculeType() {
+        return new MoleculeType();
+    }
+
+    /**
+     * Create an instance of {@link OrganismNameType }
+     * 
+     */
+    public OrganismNameType createOrganismNameType() {
+        return new OrganismNameType();
+    }
+
+    /**
+     * Create an instance of {@link SubcellularLocationType }
+     * 
+     */
+    public SubcellularLocationType createSubcellularLocationType() {
+        return new SubcellularLocationType();
+    }
+
+    /**
+     * Create an instance of {@link SourceDataType.Strain }
+     * 
+     */
+    public SourceDataType.Strain createSourceDataTypeStrain() {
+        return new SourceDataType.Strain();
+    }
+
+    /**
+     * Create an instance of {@link SourceDataType.Plasmid }
+     * 
+     */
+    public SourceDataType.Plasmid createSourceDataTypePlasmid() {
+        return new SourceDataType.Plasmid();
+    }
+
+    /**
+     * Create an instance of {@link SourceDataType.Transposon }
+     * 
+     */
+    public SourceDataType.Transposon createSourceDataTypeTransposon() {
+        return new SourceDataType.Transposon();
+    }
+
+    /**
+     * Create an instance of {@link SourceDataType.Tissue }
+     * 
+     */
+    public SourceDataType.Tissue createSourceDataTypeTissue() {
+        return new SourceDataType.Tissue();
+    }
+
+    /**
+     * Create an instance of {@link IsoformType.Name }
+     * 
+     */
+    public IsoformType.Name createIsoformTypeName() {
+        return new IsoformType.Name();
+    }
+
+    /**
+     * Create an instance of {@link IsoformType.Sequence }
+     * 
+     */
+    public IsoformType.Sequence createIsoformTypeSequence() {
+        return new IsoformType.Sequence();
+    }
+
+    /**
+     * Create an instance of {@link CommentType.Absorption }
+     * 
+     */
+    public CommentType.Absorption createCommentTypeAbsorption() {
+        return new CommentType.Absorption();
+    }
+
+    /**
+     * Create an instance of {@link CommentType.Kinetics }
+     * 
+     */
+    public CommentType.Kinetics createCommentTypeKinetics() {
+        return new CommentType.Kinetics();
+    }
+
+    /**
+     * Create an instance of {@link CommentType.PhDependence }
+     * 
+     */
+    public CommentType.PhDependence createCommentTypePhDependence() {
+        return new CommentType.PhDependence();
+    }
+
+    /**
+     * Create an instance of {@link CommentType.RedoxPotential }
+     * 
+     */
+    public CommentType.RedoxPotential createCommentTypeRedoxPotential() {
+        return new CommentType.RedoxPotential();
+    }
+
+    /**
+     * Create an instance of {@link CommentType.TemperatureDependence }
+     * 
+     */
+    public CommentType.TemperatureDependence createCommentTypeTemperatureDependence() {
+        return new CommentType.TemperatureDependence();
+    }
+
+    /**
+     * Create an instance of {@link CommentType.Link }
+     * 
+     */
+    public CommentType.Link createCommentTypeLink() {
+        return new CommentType.Link();
+    }
+
+    /**
+     * Create an instance of {@link CommentType.Disease }
+     * 
+     */
+    public CommentType.Disease createCommentTypeDisease() {
+        return new CommentType.Disease();
+    }
+
+    /**
+     * Create an instance of {@link CommentType.Conflict.Sequence }
+     * 
+     */
+    public CommentType.Conflict.Sequence createCommentTypeConflictSequence() {
+        return new CommentType.Conflict.Sequence();
+    }
+
+    /**
+     * Create an instance of {@link OrganismType.Lineage }
+     * 
+     */
+    public OrganismType.Lineage createOrganismTypeLineage() {
+        return new OrganismType.Lineage();
+    }
+
+    /**
+     * Create an instance of {@link ProteinType.RecommendedName }
+     * 
+     */
+    public ProteinType.RecommendedName createProteinTypeRecommendedName() {
+        return new ProteinType.RecommendedName();
+    }
+
+    /**
+     * Create an instance of {@link ProteinType.AlternativeName }
+     * 
+     */
+    public ProteinType.AlternativeName createProteinTypeAlternativeName() {
+        return new ProteinType.AlternativeName();
+    }
+
+    /**
+     * Create an instance of {@link ProteinType.SubmittedName }
+     * 
+     */
+    public ProteinType.SubmittedName createProteinTypeSubmittedName() {
+        return new ProteinType.SubmittedName();
+    }
+
+    /**
+     * Create an instance of {@link ProteinType.Domain }
+     * 
+     */
+    public ProteinType.Domain createProteinTypeDomain() {
+        return new ProteinType.Domain();
+    }
+
+    /**
+     * Create an instance of {@link ProteinType.Component }
+     * 
+     */
+    public ProteinType.Component createProteinTypeComponent() {
+        return new ProteinType.Component();
+    }
+
+    /**
+     * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}}
+     * 
+     */
+    @XmlElementDecl(namespace = "http://uniprot.org/uniprot", name = "copyright")
+    public JAXBElement<String> createCopyright(String value) {
+        return new JAXBElement<String>(_Copyright_QNAME, String.class, null, value);
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/OrganismNameType.java b/src/jalview/xml/binding/uniprot/OrganismNameType.java
index 5668759..5e82f4f 100644
--- a/src/jalview/xml/binding/uniprot/OrganismNameType.java
+++ b/src/jalview/xml/binding/uniprot/OrganismNameType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,15 +14,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
+
 /**
  * Describes different types of source organism names.
  * 
- * <p>
- * Java class for organismNameType complex type.
+ * <p>Java class for organismNameType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="organismNameType">
@@ -46,60 +45,62 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "organismNameType", propOrder = { "value" })
-public class OrganismNameType
-{
-
-  @XmlValue
-  protected String value;
+@XmlType(name = "organismNameType", propOrder = {
+    "value"
+})
+public class OrganismNameType {
 
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
+    @XmlValue
+    protected String value;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
 
-  /**
-   * Gets the value of the value property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getValue()
-  {
-    return value;
-  }
+    /**
+     * Gets the value of the value property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getValue() {
+        return value;
+    }
 
-  /**
-   * Sets the value of the value property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setValue(String value)
-  {
-    this.value = value;
-  }
+    /**
+     * Sets the value of the value property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setValue(String value) {
+        this.value = value;
+    }
 
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
+    /**
+     * Gets the value of the type property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getType() {
+        return type;
+    }
 
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
+    /**
+     * Sets the value of the type property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/OrganismType.java b/src/jalview/xml/binding/uniprot/OrganismType.java
index e53de4c..ca8ad97 100644
--- a/src/jalview/xml/binding/uniprot/OrganismType.java
+++ b/src/jalview/xml/binding/uniprot/OrganismType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,15 +16,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
  * Describes the source organism.
  * 
- * <p>
- * Java class for organismType complex type.
+ * <p>Java class for organismType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="organismType">
@@ -53,203 +52,190 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "organismType",
-  propOrder =
-  { "name", "dbReference", "lineage" })
-public class OrganismType
-{
-
-  @XmlElement(required = true)
-  protected List<OrganismNameType> name;
-
-  @XmlElement(required = true)
-  protected List<DbReferenceType> dbReference;
-
-  protected OrganismType.Lineage lineage;
-
-  @XmlAttribute(name = "evidence")
-  protected List<Integer> evidence;
-
-  /**
-   * Gets the value of the name property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the name property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getName().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link OrganismNameType }
-   * 
-   * 
-   */
-  public List<OrganismNameType> getName()
-  {
-    if (name == null)
-    {
-      name = new ArrayList<OrganismNameType>();
+@XmlType(name = "organismType", propOrder = {
+    "name",
+    "dbReference",
+    "lineage"
+})
+public class OrganismType {
+
+    @XmlElement(required = true)
+    protected List<OrganismNameType> name;
+    @XmlElement(required = true)
+    protected List<DbReferenceType> dbReference;
+    protected OrganismType.Lineage lineage;
+    @XmlAttribute(name = "evidence")
+    protected List<Integer> evidence;
+
+    /**
+     * Gets the value of the name property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the name property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getName().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link OrganismNameType }
+     * 
+     * 
+     */
+    public List<OrganismNameType> getName() {
+        if (name == null) {
+            name = new ArrayList<OrganismNameType>();
+        }
+        return this.name;
     }
-    return this.name;
-  }
-
-  /**
-   * Gets the value of the dbReference property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the dbReference property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getDbReference().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link DbReferenceType }
-   * 
-   * 
-   */
-  public List<DbReferenceType> getDbReference()
-  {
-    if (dbReference == null)
-    {
-      dbReference = new ArrayList<DbReferenceType>();
+
+    /**
+     * Gets the value of the dbReference property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the dbReference property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getDbReference().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link DbReferenceType }
+     * 
+     * 
+     */
+    public List<DbReferenceType> getDbReference() {
+        if (dbReference == null) {
+            dbReference = new ArrayList<DbReferenceType>();
+        }
+        return this.dbReference;
     }
-    return this.dbReference;
-  }
-
-  /**
-   * Gets the value of the lineage property.
-   * 
-   * @return possible object is {@link OrganismType.Lineage }
-   * 
-   */
-  public OrganismType.Lineage getLineage()
-  {
-    return lineage;
-  }
-
-  /**
-   * Sets the value of the lineage property.
-   * 
-   * @param value
-   *          allowed object is {@link OrganismType.Lineage }
-   * 
-   */
-  public void setLineage(OrganismType.Lineage value)
-  {
-    this.lineage = value;
-  }
-
-  /**
-   * Gets the value of the evidence property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the evidence property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getEvidence().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List<Integer> getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList<Integer>();
+
+    /**
+     * Gets the value of the lineage property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link OrganismType.Lineage }
+     *     
+     */
+    public OrganismType.Lineage getLineage() {
+        return lineage;
     }
-    return this.evidence;
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;sequence>
-   *         &lt;element name="taxon" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
-   *       &lt;/sequence>
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "taxon" })
-  public static class Lineage
-  {
 
-    @XmlElement(required = true)
-    protected List<String> taxon;
+    /**
+     * Sets the value of the lineage property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link OrganismType.Lineage }
+     *     
+     */
+    public void setLineage(OrganismType.Lineage value) {
+        this.lineage = value;
+    }
 
     /**
-     * Gets the value of the taxon property.
+     * Gets the value of the evidence property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the taxon property.
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the evidence property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
-     * 
      * <pre>
-     * getTaxon().add(newItem);
+     *    getEvidence().add(newItem);
      * </pre>
      * 
      * 
      * <p>
-     * Objects of the following type(s) are allowed in the list {@link String }
+     * Objects of the following type(s) are allowed in the list
+     * {@link Integer }
      * 
      * 
      */
-    public List<String> getTaxon()
-    {
-      if (taxon == null)
-      {
-        taxon = new ArrayList<String>();
-      }
-      return this.taxon;
+    public List<Integer> getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList<Integer>();
+        }
+        return this.evidence;
     }
 
-  }
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="taxon" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+     *       &lt;/sequence>
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "taxon"
+    })
+    public static class Lineage {
+
+        @XmlElement(required = true)
+        protected List<String> taxon;
+
+        /**
+         * Gets the value of the taxon property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the taxon property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getTaxon().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link String }
+         * 
+         * 
+         */
+        public List<String> getTaxon() {
+            if (taxon == null) {
+                taxon = new ArrayList<String>();
+            }
+            return this.taxon;
+        }
+
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/PersonType.java b/src/jalview/xml/binding/uniprot/PersonType.java
index ebbb691..4639054 100644
--- a/src/jalview/xml/binding/uniprot/PersonType.java
+++ b/src/jalview/xml/binding/uniprot/PersonType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,13 +13,11 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>
- * Java class for personType complex type.
+ * <p>Java class for personType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="personType">
@@ -34,33 +33,33 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "personType")
-public class PersonType
-{
+public class PersonType {
 
-  @XmlAttribute(name = "name", required = true)
-  protected String name;
+    @XmlAttribute(name = "name", required = true)
+    protected String name;
 
-  /**
-   * Gets the value of the name property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getName()
-  {
-    return name;
-  }
+    /**
+     * Gets the value of the name property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getName() {
+        return name;
+    }
 
-  /**
-   * Sets the value of the name property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setName(String value)
-  {
-    this.name = value;
-  }
+    /**
+     * Sets the value of the name property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setName(String value) {
+        this.name = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java b/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java
index 95298e4..b01e412 100644
--- a/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java
+++ b/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,15 +16,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
  * Describes a physiological reaction.
  * 
- * <p>
- * Java class for physiologicalReactionType complex type.
+ * <p>Java class for physiologicalReactionType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="physiologicalReactionType">
@@ -49,94 +48,93 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "physiologicalReactionType", propOrder = { "dbReference" })
-public class PhysiologicalReactionType
-{
-
-  @XmlElement(required = true)
-  protected DbReferenceType dbReference;
-
-  @XmlAttribute(name = "direction", required = true)
-  protected String direction;
+@XmlType(name = "physiologicalReactionType", propOrder = {
+    "dbReference"
+})
+public class PhysiologicalReactionType {
 
-  @XmlAttribute(name = "evidence")
-  protected List<Integer> evidence;
+    @XmlElement(required = true)
+    protected DbReferenceType dbReference;
+    @XmlAttribute(name = "direction", required = true)
+    protected String direction;
+    @XmlAttribute(name = "evidence")
+    protected List<Integer> evidence;
 
-  /**
-   * Gets the value of the dbReference property.
-   * 
-   * @return possible object is {@link DbReferenceType }
-   * 
-   */
-  public DbReferenceType getDbReference()
-  {
-    return dbReference;
-  }
+    /**
+     * Gets the value of the dbReference property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link DbReferenceType }
+     *     
+     */
+    public DbReferenceType getDbReference() {
+        return dbReference;
+    }
 
-  /**
-   * Sets the value of the dbReference property.
-   * 
-   * @param value
-   *          allowed object is {@link DbReferenceType }
-   * 
-   */
-  public void setDbReference(DbReferenceType value)
-  {
-    this.dbReference = value;
-  }
+    /**
+     * Sets the value of the dbReference property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link DbReferenceType }
+     *     
+     */
+    public void setDbReference(DbReferenceType value) {
+        this.dbReference = value;
+    }
 
-  /**
-   * Gets the value of the direction property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDirection()
-  {
-    return direction;
-  }
+    /**
+     * Gets the value of the direction property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDirection() {
+        return direction;
+    }
 
-  /**
-   * Sets the value of the direction property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDirection(String value)
-  {
-    this.direction = value;
-  }
+    /**
+     * Sets the value of the direction property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDirection(String value) {
+        this.direction = value;
+    }
 
-  /**
-   * Gets the value of the evidence property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the evidence property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getEvidence().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List<Integer> getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList<Integer>();
+    /**
+     * Gets the value of the evidence property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the evidence property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getEvidence().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link Integer }
+     * 
+     * 
+     */
+    public List<Integer> getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList<Integer>();
+        }
+        return this.evidence;
     }
-    return this.evidence;
-  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/PositionType.java b/src/jalview/xml/binding/uniprot/PositionType.java
index c3713fa..25d6030 100644
--- a/src/jalview/xml/binding/uniprot/PositionType.java
+++ b/src/jalview/xml/binding/uniprot/PositionType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.math.BigInteger;
@@ -16,13 +17,11 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlSchemaType;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>
- * Java class for positionType complex type.
+ * <p>Java class for positionType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="positionType">
@@ -50,101 +49,95 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "positionType")
-public class PositionType
-{
-
-  @XmlAttribute(name = "position")
-  @XmlSchemaType(name = "unsignedLong")
-  protected BigInteger position;
-
-  @XmlAttribute(name = "status")
-  protected String status;
+public class PositionType {
 
-  @XmlAttribute(name = "evidence")
-  protected List<Integer> evidence;
+    @XmlAttribute(name = "position")
+    @XmlSchemaType(name = "unsignedLong")
+    protected BigInteger position;
+    @XmlAttribute(name = "status")
+    protected String status;
+    @XmlAttribute(name = "evidence")
+    protected List<Integer> evidence;
 
-  /**
-   * Gets the value of the position property.
-   * 
-   * @return possible object is {@link BigInteger }
-   * 
-   */
-  public BigInteger getPosition()
-  {
-    return position;
-  }
-
-  /**
-   * Sets the value of the position property.
-   * 
-   * @param value
-   *          allowed object is {@link BigInteger }
-   * 
-   */
-  public void setPosition(BigInteger value)
-  {
-    this.position = value;
-  }
+    /**
+     * Gets the value of the position property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link BigInteger }
+     *     
+     */
+    public BigInteger getPosition() {
+        return position;
+    }
 
-  /**
-   * Gets the value of the status property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getStatus()
-  {
-    if (status == null)
-    {
-      return "certain";
+    /**
+     * Sets the value of the position property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link BigInteger }
+     *     
+     */
+    public void setPosition(BigInteger value) {
+        this.position = value;
     }
-    else
-    {
-      return status;
+
+    /**
+     * Gets the value of the status property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getStatus() {
+        if (status == null) {
+            return "certain";
+        } else {
+            return status;
+        }
     }
-  }
 
-  /**
-   * Sets the value of the status property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setStatus(String value)
-  {
-    this.status = value;
-  }
+    /**
+     * Sets the value of the status property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setStatus(String value) {
+        this.status = value;
+    }
 
-  /**
-   * Gets the value of the evidence property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the evidence property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getEvidence().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List<Integer> getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList<Integer>();
+    /**
+     * Gets the value of the evidence property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the evidence property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getEvidence().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link Integer }
+     * 
+     * 
+     */
+    public List<Integer> getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList<Integer>();
+        }
+        return this.evidence;
     }
-    return this.evidence;
-  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/PropertyType.java b/src/jalview/xml/binding/uniprot/PropertyType.java
index 6b43149..b1ab0f3 100644
--- a/src/jalview/xml/binding/uniprot/PropertyType.java
+++ b/src/jalview/xml/binding/uniprot/PropertyType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,13 +13,11 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>
- * Java class for propertyType complex type.
+ * <p>Java class for propertyType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="propertyType">
@@ -35,59 +34,59 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "propertyType")
-public class PropertyType
-{
-
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
+public class PropertyType {
 
-  @XmlAttribute(name = "value", required = true)
-  protected String value;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
+    @XmlAttribute(name = "value", required = true)
+    protected String value;
 
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
+    /**
+     * Gets the value of the type property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getType() {
+        return type;
+    }
 
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
+    /**
+     * Sets the value of the type property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
 
-  /**
-   * Gets the value of the value property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getValue()
-  {
-    return value;
-  }
+    /**
+     * Gets the value of the value property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getValue() {
+        return value;
+    }
 
-  /**
-   * Sets the value of the value property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setValue(String value)
-  {
-    this.value = value;
-  }
+    /**
+     * Sets the value of the value property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setValue(String value) {
+        this.value = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/ProteinExistenceType.java b/src/jalview/xml/binding/uniprot/ProteinExistenceType.java
index 3d07edb..73f4c21 100644
--- a/src/jalview/xml/binding/uniprot/ProteinExistenceType.java
+++ b/src/jalview/xml/binding/uniprot/ProteinExistenceType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,16 +13,14 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes the evidence for the protein's existence. Equivalent to the flat
- * file PE-line.
+ * Describes the evidence for the protein's existence.
+ *             Equivalent to the flat file PE-line.
  * 
- * <p>
- * Java class for proteinExistenceType complex type.
+ * <p>Java class for proteinExistenceType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="proteinExistenceType">
@@ -47,33 +46,33 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "proteinExistenceType")
-public class ProteinExistenceType
-{
+public class ProteinExistenceType {
 
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
 
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
+    /**
+     * Gets the value of the type property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getType() {
+        return type;
+    }
 
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
+    /**
+     * Sets the value of the type property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/ProteinType.java b/src/jalview/xml/binding/uniprot/ProteinType.java
index 5a7d731..f3d0e80 100644
--- a/src/jalview/xml/binding/uniprot/ProteinType.java
+++ b/src/jalview/xml/binding/uniprot/ProteinType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -14,16 +15,14 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes the names for the protein and parts thereof. Equivalent to the flat
- * file DE-line.
+ * Describes the names for the protein and parts thereof.
+ *             Equivalent to the flat file DE-line.
  * 
- * <p>
- * Java class for proteinType complex type.
+ * <p>Java class for proteinType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="proteinType">
@@ -58,497 +57,66 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "proteinType",
-  propOrder =
-  { "recommendedName", "alternativeName", "submittedName", "allergenName",
-      "biotechName", "cdAntigenName", "innName", "domain", "component" })
-public class ProteinType
-{
-
-  protected ProteinType.RecommendedName recommendedName;
-
-  protected List<ProteinType.AlternativeName> alternativeName;
-
-  protected List<ProteinType.SubmittedName> submittedName;
-
-  protected EvidencedStringType allergenName;
-
-  protected EvidencedStringType biotechName;
-
-  protected List<EvidencedStringType> cdAntigenName;
-
-  protected List<EvidencedStringType> innName;
-
-  protected List<ProteinType.Domain> domain;
-
-  protected List<ProteinType.Component> component;
-
-  /**
-   * Gets the value of the recommendedName property.
-   * 
-   * @return possible object is {@link ProteinType.RecommendedName }
-   * 
-   */
-  public ProteinType.RecommendedName getRecommendedName()
-  {
-    return recommendedName;
-  }
-
-  /**
-   * Sets the value of the recommendedName property.
-   * 
-   * @param value
-   *          allowed object is {@link ProteinType.RecommendedName }
-   * 
-   */
-  public void setRecommendedName(ProteinType.RecommendedName value)
-  {
-    this.recommendedName = value;
-  }
-
-  /**
-   * Gets the value of the alternativeName property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the alternativeName property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getAlternativeName().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link ProteinType.AlternativeName }
-   * 
-   * 
-   */
-  public List<ProteinType.AlternativeName> getAlternativeName()
-  {
-    if (alternativeName == null)
-    {
-      alternativeName = new ArrayList<ProteinType.AlternativeName>();
-    }
-    return this.alternativeName;
-  }
-
-  /**
-   * Gets the value of the submittedName property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the submittedName property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getSubmittedName().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link ProteinType.SubmittedName }
-   * 
-   * 
-   */
-  public List<ProteinType.SubmittedName> getSubmittedName()
-  {
-    if (submittedName == null)
-    {
-      submittedName = new ArrayList<ProteinType.SubmittedName>();
-    }
-    return this.submittedName;
-  }
-
-  /**
-   * Gets the value of the allergenName property.
-   * 
-   * @return possible object is {@link EvidencedStringType }
-   * 
-   */
-  public EvidencedStringType getAllergenName()
-  {
-    return allergenName;
-  }
-
-  /**
-   * Sets the value of the allergenName property.
-   * 
-   * @param value
-   *          allowed object is {@link EvidencedStringType }
-   * 
-   */
-  public void setAllergenName(EvidencedStringType value)
-  {
-    this.allergenName = value;
-  }
-
-  /**
-   * Gets the value of the biotechName property.
-   * 
-   * @return possible object is {@link EvidencedStringType }
-   * 
-   */
-  public EvidencedStringType getBiotechName()
-  {
-    return biotechName;
-  }
-
-  /**
-   * Sets the value of the biotechName property.
-   * 
-   * @param value
-   *          allowed object is {@link EvidencedStringType }
-   * 
-   */
-  public void setBiotechName(EvidencedStringType value)
-  {
-    this.biotechName = value;
-  }
-
-  /**
-   * Gets the value of the cdAntigenName property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the cdAntigenName property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getCdAntigenName().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link EvidencedStringType }
-   * 
-   * 
-   */
-  public List<EvidencedStringType> getCdAntigenName()
-  {
-    if (cdAntigenName == null)
-    {
-      cdAntigenName = new ArrayList<EvidencedStringType>();
-    }
-    return this.cdAntigenName;
-  }
-
-  /**
-   * Gets the value of the innName property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the innName property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getInnName().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link EvidencedStringType }
-   * 
-   * 
-   */
-  public List<EvidencedStringType> getInnName()
-  {
-    if (innName == null)
-    {
-      innName = new ArrayList<EvidencedStringType>();
-    }
-    return this.innName;
-  }
-
-  /**
-   * Gets the value of the domain property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the domain property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getDomain().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link ProteinType.Domain }
-   * 
-   * 
-   */
-  public List<ProteinType.Domain> getDomain()
-  {
-    if (domain == null)
-    {
-      domain = new ArrayList<ProteinType.Domain>();
-    }
-    return this.domain;
-  }
-
-  /**
-   * Gets the value of the component property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the component property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getComponent().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link ProteinType.Component }
-   * 
-   * 
-   */
-  public List<ProteinType.Component> getComponent()
-  {
-    if (component == null)
-    {
-      component = new ArrayList<ProteinType.Component>();
-    }
-    return this.component;
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;sequence>
-   *         &lt;element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
-   *         &lt;element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-   *         &lt;element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-   *       &lt;/sequence>
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "fullName", "shortName", "ecNumber" })
-  public static class AlternativeName
-  {
-
-    protected EvidencedStringType fullName;
-
-    protected List<EvidencedStringType> shortName;
-
-    protected List<EvidencedStringType> ecNumber;
-
-    /**
-     * Gets the value of the fullName property.
-     * 
-     * @return possible object is {@link EvidencedStringType }
-     * 
-     */
-    public EvidencedStringType getFullName()
-    {
-      return fullName;
-    }
-
-    /**
-     * Sets the value of the fullName property.
-     * 
-     * @param value
-     *          allowed object is {@link EvidencedStringType }
-     * 
-     */
-    public void setFullName(EvidencedStringType value)
-    {
-      this.fullName = value;
-    }
-
-    /**
-     * Gets the value of the shortName property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the shortName property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * 
-     * <pre>
-     * getShortName().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
-     * 
-     * 
-     */
-    public List<EvidencedStringType> getShortName()
-    {
-      if (shortName == null)
-      {
-        shortName = new ArrayList<EvidencedStringType>();
-      }
-      return this.shortName;
-    }
-
-    /**
-     * Gets the value of the ecNumber property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the ecNumber property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * 
-     * <pre>
-     * getEcNumber().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
-     * 
-     * 
-     */
-    public List<EvidencedStringType> getEcNumber()
-    {
-      if (ecNumber == null)
-      {
-        ecNumber = new ArrayList<EvidencedStringType>();
-      }
-      return this.ecNumber;
-    }
-
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(
-    name = "",
-    propOrder =
-    { "recommendedName", "alternativeName", "submittedName", "allergenName",
-        "biotechName", "cdAntigenName", "innName" })
-  public static class Component
-  {
+@XmlType(name = "proteinType", propOrder = {
+    "recommendedName",
+    "alternativeName",
+    "submittedName",
+    "allergenName",
+    "biotechName",
+    "cdAntigenName",
+    "innName",
+    "domain",
+    "component"
+})
+public class ProteinType {
 
     protected ProteinType.RecommendedName recommendedName;
-
     protected List<ProteinType.AlternativeName> alternativeName;
-
     protected List<ProteinType.SubmittedName> submittedName;
-
     protected EvidencedStringType allergenName;
-
     protected EvidencedStringType biotechName;
-
     protected List<EvidencedStringType> cdAntigenName;
-
     protected List<EvidencedStringType> innName;
+    protected List<ProteinType.Domain> domain;
+    protected List<ProteinType.Component> component;
 
     /**
      * Gets the value of the recommendedName property.
      * 
-     * @return possible object is {@link ProteinType.RecommendedName }
-     * 
+     * @return
+     *     possible object is
+     *     {@link ProteinType.RecommendedName }
+     *     
      */
-    public ProteinType.RecommendedName getRecommendedName()
-    {
-      return recommendedName;
+    public ProteinType.RecommendedName getRecommendedName() {
+        return recommendedName;
     }
 
     /**
      * Sets the value of the recommendedName property.
      * 
      * @param value
-     *          allowed object is {@link ProteinType.RecommendedName }
-     * 
+     *     allowed object is
+     *     {@link ProteinType.RecommendedName }
+     *     
      */
-    public void setRecommendedName(ProteinType.RecommendedName value)
-    {
-      this.recommendedName = value;
+    public void setRecommendedName(ProteinType.RecommendedName value) {
+        this.recommendedName = value;
     }
 
     /**
      * Gets the value of the alternativeName property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the alternativeName property.
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the alternativeName property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
-     * 
      * <pre>
-     * getAlternativeName().add(newItem);
+     *    getAlternativeName().add(newItem);
      * </pre>
      * 
      * 
@@ -558,29 +126,26 @@ public class ProteinType
      * 
      * 
      */
-    public List<ProteinType.AlternativeName> getAlternativeName()
-    {
-      if (alternativeName == null)
-      {
-        alternativeName = new ArrayList<ProteinType.AlternativeName>();
-      }
-      return this.alternativeName;
+    public List<ProteinType.AlternativeName> getAlternativeName() {
+        if (alternativeName == null) {
+            alternativeName = new ArrayList<ProteinType.AlternativeName>();
+        }
+        return this.alternativeName;
     }
 
     /**
      * Gets the value of the submittedName property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the submittedName property.
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the submittedName property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
-     * 
      * <pre>
-     * getSubmittedName().add(newItem);
+     *    getSubmittedName().add(newItem);
      * </pre>
      * 
      * 
@@ -590,75 +155,74 @@ public class ProteinType
      * 
      * 
      */
-    public List<ProteinType.SubmittedName> getSubmittedName()
-    {
-      if (submittedName == null)
-      {
-        submittedName = new ArrayList<ProteinType.SubmittedName>();
-      }
-      return this.submittedName;
+    public List<ProteinType.SubmittedName> getSubmittedName() {
+        if (submittedName == null) {
+            submittedName = new ArrayList<ProteinType.SubmittedName>();
+        }
+        return this.submittedName;
     }
 
     /**
      * Gets the value of the allergenName property.
      * 
-     * @return possible object is {@link EvidencedStringType }
-     * 
+     * @return
+     *     possible object is
+     *     {@link EvidencedStringType }
+     *     
      */
-    public EvidencedStringType getAllergenName()
-    {
-      return allergenName;
+    public EvidencedStringType getAllergenName() {
+        return allergenName;
     }
 
     /**
      * Sets the value of the allergenName property.
      * 
      * @param value
-     *          allowed object is {@link EvidencedStringType }
-     * 
+     *     allowed object is
+     *     {@link EvidencedStringType }
+     *     
      */
-    public void setAllergenName(EvidencedStringType value)
-    {
-      this.allergenName = value;
+    public void setAllergenName(EvidencedStringType value) {
+        this.allergenName = value;
     }
 
     /**
      * Gets the value of the biotechName property.
      * 
-     * @return possible object is {@link EvidencedStringType }
-     * 
+     * @return
+     *     possible object is
+     *     {@link EvidencedStringType }
+     *     
      */
-    public EvidencedStringType getBiotechName()
-    {
-      return biotechName;
+    public EvidencedStringType getBiotechName() {
+        return biotechName;
     }
 
     /**
      * Sets the value of the biotechName property.
      * 
      * @param value
-     *          allowed object is {@link EvidencedStringType }
-     * 
+     *     allowed object is
+     *     {@link EvidencedStringType }
+     *     
      */
-    public void setBiotechName(EvidencedStringType value)
-    {
-      this.biotechName = value;
+    public void setBiotechName(EvidencedStringType value) {
+        this.biotechName = value;
     }
 
     /**
      * Gets the value of the cdAntigenName property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the cdAntigenName property.
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the cdAntigenName property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
-     * 
      * <pre>
-     * getCdAntigenName().add(newItem);
+     *    getCdAntigenName().add(newItem);
      * </pre>
      * 
      * 
@@ -668,29 +232,26 @@ public class ProteinType
      * 
      * 
      */
-    public List<EvidencedStringType> getCdAntigenName()
-    {
-      if (cdAntigenName == null)
-      {
-        cdAntigenName = new ArrayList<EvidencedStringType>();
-      }
-      return this.cdAntigenName;
+    public List<EvidencedStringType> getCdAntigenName() {
+        if (cdAntigenName == null) {
+            cdAntigenName = new ArrayList<EvidencedStringType>();
+        }
+        return this.cdAntigenName;
     }
 
     /**
      * Gets the value of the innName property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the innName property.
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the innName property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
-     * 
      * <pre>
-     * getInnName().add(newItem);
+     *    getInnName().add(newItem);
      * </pre>
      * 
      * 
@@ -700,472 +261,849 @@ public class ProteinType
      * 
      * 
      */
-    public List<EvidencedStringType> getInnName()
-    {
-      if (innName == null)
-      {
-        innName = new ArrayList<EvidencedStringType>();
-      }
-      return this.innName;
-    }
-
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(
-    name = "",
-    propOrder =
-    { "recommendedName", "alternativeName", "submittedName", "allergenName",
-        "biotechName", "cdAntigenName", "innName" })
-  public static class Domain
-  {
-
-    protected ProteinType.RecommendedName recommendedName;
-
-    protected List<ProteinType.AlternativeName> alternativeName;
-
-    protected List<ProteinType.SubmittedName> submittedName;
-
-    protected EvidencedStringType allergenName;
-
-    protected EvidencedStringType biotechName;
-
-    protected List<EvidencedStringType> cdAntigenName;
-
-    protected List<EvidencedStringType> innName;
-
-    /**
-     * Gets the value of the recommendedName property.
-     * 
-     * @return possible object is {@link ProteinType.RecommendedName }
-     * 
-     */
-    public ProteinType.RecommendedName getRecommendedName()
-    {
-      return recommendedName;
+    public List<EvidencedStringType> getInnName() {
+        if (innName == null) {
+            innName = new ArrayList<EvidencedStringType>();
+        }
+        return this.innName;
     }
 
     /**
-     * Sets the value of the recommendedName property.
-     * 
-     * @param value
-     *          allowed object is {@link ProteinType.RecommendedName }
-     * 
-     */
-    public void setRecommendedName(ProteinType.RecommendedName value)
-    {
-      this.recommendedName = value;
-    }
-
-    /**
-     * Gets the value of the alternativeName property.
+     * Gets the value of the domain property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the alternativeName property.
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the domain property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
-     * 
      * <pre>
-     * getAlternativeName().add(newItem);
+     *    getDomain().add(newItem);
      * </pre>
      * 
      * 
      * <p>
      * Objects of the following type(s) are allowed in the list
-     * {@link ProteinType.AlternativeName }
+     * {@link ProteinType.Domain }
      * 
      * 
      */
-    public List<ProteinType.AlternativeName> getAlternativeName()
-    {
-      if (alternativeName == null)
-      {
-        alternativeName = new ArrayList<ProteinType.AlternativeName>();
-      }
-      return this.alternativeName;
+    public List<ProteinType.Domain> getDomain() {
+        if (domain == null) {
+            domain = new ArrayList<ProteinType.Domain>();
+        }
+        return this.domain;
     }
 
     /**
-     * Gets the value of the submittedName property.
+     * Gets the value of the component property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the submittedName property.
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the component property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
-     * 
      * <pre>
-     * getSubmittedName().add(newItem);
+     *    getComponent().add(newItem);
      * </pre>
      * 
      * 
      * <p>
      * Objects of the following type(s) are allowed in the list
-     * {@link ProteinType.SubmittedName }
-     * 
-     * 
-     */
-    public List<ProteinType.SubmittedName> getSubmittedName()
-    {
-      if (submittedName == null)
-      {
-        submittedName = new ArrayList<ProteinType.SubmittedName>();
-      }
-      return this.submittedName;
-    }
-
-    /**
-     * Gets the value of the allergenName property.
-     * 
-     * @return possible object is {@link EvidencedStringType }
-     * 
-     */
-    public EvidencedStringType getAllergenName()
-    {
-      return allergenName;
-    }
-
-    /**
-     * Sets the value of the allergenName property.
+     * {@link ProteinType.Component }
      * 
-     * @param value
-     *          allowed object is {@link EvidencedStringType }
      * 
      */
-    public void setAllergenName(EvidencedStringType value)
-    {
-      this.allergenName = value;
+    public List<ProteinType.Component> getComponent() {
+        if (component == null) {
+            component = new ArrayList<ProteinType.Component>();
+        }
+        return this.component;
     }
 
-    /**
-     * Gets the value of the biotechName property.
-     * 
-     * @return possible object is {@link EvidencedStringType }
-     * 
-     */
-    public EvidencedStringType getBiotechName()
-    {
-      return biotechName;
-    }
 
     /**
-     * Sets the value of the biotechName property.
+     * <p>Java class for anonymous complex type.
      * 
-     * @param value
-     *          allowed object is {@link EvidencedStringType }
-     * 
-     */
-    public void setBiotechName(EvidencedStringType value)
-    {
-      this.biotechName = value;
-    }
-
-    /**
-     * Gets the value of the cdAntigenName property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the cdAntigenName property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * <p>The following schema fragment specifies the expected content contained within this class.
      * 
      * <pre>
-     * getCdAntigenName().add(newItem);
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
+     *         &lt;element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+     *         &lt;element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+     *       &lt;/sequence>
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
      * </pre>
      * 
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
-     * 
-     * 
      */
-    public List<EvidencedStringType> getCdAntigenName()
-    {
-      if (cdAntigenName == null)
-      {
-        cdAntigenName = new ArrayList<EvidencedStringType>();
-      }
-      return this.cdAntigenName;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "fullName",
+        "shortName",
+        "ecNumber"
+    })
+    public static class AlternativeName {
+
+        protected EvidencedStringType fullName;
+        protected List<EvidencedStringType> shortName;
+        protected List<EvidencedStringType> ecNumber;
+
+        /**
+         * Gets the value of the fullName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public EvidencedStringType getFullName() {
+            return fullName;
+        }
+
+        /**
+         * Sets the value of the fullName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public void setFullName(EvidencedStringType value) {
+            this.fullName = value;
+        }
+
+        /**
+         * Gets the value of the shortName property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the shortName property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getShortName().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List<EvidencedStringType> getShortName() {
+            if (shortName == null) {
+                shortName = new ArrayList<EvidencedStringType>();
+            }
+            return this.shortName;
+        }
+
+        /**
+         * Gets the value of the ecNumber property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the ecNumber property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getEcNumber().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List<EvidencedStringType> getEcNumber() {
+            if (ecNumber == null) {
+                ecNumber = new ArrayList<EvidencedStringType>();
+            }
+            return this.ecNumber;
+        }
+
     }
 
+
     /**
-     * Gets the value of the innName property.
+     * <p>Java class for anonymous complex type.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the innName property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * <p>The following schema fragment specifies the expected content contained within this class.
      * 
      * <pre>
-     * getInnName().add(newItem);
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
      * </pre>
      * 
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
-     * 
-     * 
      */
-    public List<EvidencedStringType> getInnName()
-    {
-      if (innName == null)
-      {
-        innName = new ArrayList<EvidencedStringType>();
-      }
-      return this.innName;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "recommendedName",
+        "alternativeName",
+        "submittedName",
+        "allergenName",
+        "biotechName",
+        "cdAntigenName",
+        "innName"
+    })
+    public static class Component {
+
+        protected ProteinType.RecommendedName recommendedName;
+        protected List<ProteinType.AlternativeName> alternativeName;
+        protected List<ProteinType.SubmittedName> submittedName;
+        protected EvidencedStringType allergenName;
+        protected EvidencedStringType biotechName;
+        protected List<EvidencedStringType> cdAntigenName;
+        protected List<EvidencedStringType> innName;
+
+        /**
+         * Gets the value of the recommendedName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link ProteinType.RecommendedName }
+         *     
+         */
+        public ProteinType.RecommendedName getRecommendedName() {
+            return recommendedName;
+        }
+
+        /**
+         * Sets the value of the recommendedName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link ProteinType.RecommendedName }
+         *     
+         */
+        public void setRecommendedName(ProteinType.RecommendedName value) {
+            this.recommendedName = value;
+        }
+
+        /**
+         * Gets the value of the alternativeName property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the alternativeName property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getAlternativeName().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link ProteinType.AlternativeName }
+         * 
+         * 
+         */
+        public List<ProteinType.AlternativeName> getAlternativeName() {
+            if (alternativeName == null) {
+                alternativeName = new ArrayList<ProteinType.AlternativeName>();
+            }
+            return this.alternativeName;
+        }
+
+        /**
+         * Gets the value of the submittedName property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the submittedName property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getSubmittedName().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link ProteinType.SubmittedName }
+         * 
+         * 
+         */
+        public List<ProteinType.SubmittedName> getSubmittedName() {
+            if (submittedName == null) {
+                submittedName = new ArrayList<ProteinType.SubmittedName>();
+            }
+            return this.submittedName;
+        }
+
+        /**
+         * Gets the value of the allergenName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public EvidencedStringType getAllergenName() {
+            return allergenName;
+        }
+
+        /**
+         * Sets the value of the allergenName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public void setAllergenName(EvidencedStringType value) {
+            this.allergenName = value;
+        }
+
+        /**
+         * Gets the value of the biotechName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public EvidencedStringType getBiotechName() {
+            return biotechName;
+        }
+
+        /**
+         * Sets the value of the biotechName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public void setBiotechName(EvidencedStringType value) {
+            this.biotechName = value;
+        }
+
+        /**
+         * Gets the value of the cdAntigenName property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the cdAntigenName property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getCdAntigenName().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List<EvidencedStringType> getCdAntigenName() {
+            if (cdAntigenName == null) {
+                cdAntigenName = new ArrayList<EvidencedStringType>();
+            }
+            return this.cdAntigenName;
+        }
+
+        /**
+         * Gets the value of the innName property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the innName property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getInnName().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List<EvidencedStringType> getInnName() {
+            if (innName == null) {
+                innName = new ArrayList<EvidencedStringType>();
+            }
+            return this.innName;
+        }
 
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;sequence>
-   *         &lt;element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
-   *         &lt;element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-   *         &lt;element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-   *       &lt;/sequence>
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "fullName", "shortName", "ecNumber" })
-  public static class RecommendedName
-  {
-
-    @XmlElement(required = true)
-    protected EvidencedStringType fullName;
-
-    protected List<EvidencedStringType> shortName;
-
-    protected List<EvidencedStringType> ecNumber;
-
-    /**
-     * Gets the value of the fullName property.
-     * 
-     * @return possible object is {@link EvidencedStringType }
-     * 
-     */
-    public EvidencedStringType getFullName()
-    {
-      return fullName;
     }
 
-    /**
-     * Sets the value of the fullName property.
-     * 
-     * @param value
-     *          allowed object is {@link EvidencedStringType }
-     * 
-     */
-    public void setFullName(EvidencedStringType value)
-    {
-      this.fullName = value;
-    }
 
     /**
-     * Gets the value of the shortName property.
+     * <p>Java class for anonymous complex type.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the shortName property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * <p>The following schema fragment specifies the expected content contained within this class.
      * 
      * <pre>
-     * getShortName().add(newItem);
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
      * </pre>
      * 
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
-     * 
-     * 
      */
-    public List<EvidencedStringType> getShortName()
-    {
-      if (shortName == null)
-      {
-        shortName = new ArrayList<EvidencedStringType>();
-      }
-      return this.shortName;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "recommendedName",
+        "alternativeName",
+        "submittedName",
+        "allergenName",
+        "biotechName",
+        "cdAntigenName",
+        "innName"
+    })
+    public static class Domain {
+
+        protected ProteinType.RecommendedName recommendedName;
+        protected List<ProteinType.AlternativeName> alternativeName;
+        protected List<ProteinType.SubmittedName> submittedName;
+        protected EvidencedStringType allergenName;
+        protected EvidencedStringType biotechName;
+        protected List<EvidencedStringType> cdAntigenName;
+        protected List<EvidencedStringType> innName;
+
+        /**
+         * Gets the value of the recommendedName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link ProteinType.RecommendedName }
+         *     
+         */
+        public ProteinType.RecommendedName getRecommendedName() {
+            return recommendedName;
+        }
+
+        /**
+         * Sets the value of the recommendedName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link ProteinType.RecommendedName }
+         *     
+         */
+        public void setRecommendedName(ProteinType.RecommendedName value) {
+            this.recommendedName = value;
+        }
+
+        /**
+         * Gets the value of the alternativeName property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the alternativeName property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getAlternativeName().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link ProteinType.AlternativeName }
+         * 
+         * 
+         */
+        public List<ProteinType.AlternativeName> getAlternativeName() {
+            if (alternativeName == null) {
+                alternativeName = new ArrayList<ProteinType.AlternativeName>();
+            }
+            return this.alternativeName;
+        }
+
+        /**
+         * Gets the value of the submittedName property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the submittedName property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getSubmittedName().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link ProteinType.SubmittedName }
+         * 
+         * 
+         */
+        public List<ProteinType.SubmittedName> getSubmittedName() {
+            if (submittedName == null) {
+                submittedName = new ArrayList<ProteinType.SubmittedName>();
+            }
+            return this.submittedName;
+        }
+
+        /**
+         * Gets the value of the allergenName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public EvidencedStringType getAllergenName() {
+            return allergenName;
+        }
+
+        /**
+         * Sets the value of the allergenName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public void setAllergenName(EvidencedStringType value) {
+            this.allergenName = value;
+        }
+
+        /**
+         * Gets the value of the biotechName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public EvidencedStringType getBiotechName() {
+            return biotechName;
+        }
+
+        /**
+         * Sets the value of the biotechName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public void setBiotechName(EvidencedStringType value) {
+            this.biotechName = value;
+        }
+
+        /**
+         * Gets the value of the cdAntigenName property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the cdAntigenName property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getCdAntigenName().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List<EvidencedStringType> getCdAntigenName() {
+            if (cdAntigenName == null) {
+                cdAntigenName = new ArrayList<EvidencedStringType>();
+            }
+            return this.cdAntigenName;
+        }
+
+        /**
+         * Gets the value of the innName property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the innName property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getInnName().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List<EvidencedStringType> getInnName() {
+            if (innName == null) {
+                innName = new ArrayList<EvidencedStringType>();
+            }
+            return this.innName;
+        }
+
     }
 
+
     /**
-     * Gets the value of the ecNumber property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the ecNumber property.
+     * <p>Java class for anonymous complex type.
      * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * <p>The following schema fragment specifies the expected content contained within this class.
      * 
      * <pre>
-     * getEcNumber().add(newItem);
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
+     *         &lt;element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+     *         &lt;element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+     *       &lt;/sequence>
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
      * </pre>
      * 
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
-     * 
-     * 
      */
-    public List<EvidencedStringType> getEcNumber()
-    {
-      if (ecNumber == null)
-      {
-        ecNumber = new ArrayList<EvidencedStringType>();
-      }
-      return this.ecNumber;
-    }
-
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;complexContent>
-   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       &lt;sequence>
-   *         &lt;element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
-   *         &lt;element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-   *       &lt;/sequence>
-   *     &lt;/restriction>
-   *   &lt;/complexContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "fullName", "ecNumber" })
-  public static class SubmittedName
-  {
-
-    @XmlElement(required = true)
-    protected EvidencedStringType fullName;
-
-    protected List<EvidencedStringType> ecNumber;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "fullName",
+        "shortName",
+        "ecNumber"
+    })
+    public static class RecommendedName {
+
+        @XmlElement(required = true)
+        protected EvidencedStringType fullName;
+        protected List<EvidencedStringType> shortName;
+        protected List<EvidencedStringType> ecNumber;
+
+        /**
+         * Gets the value of the fullName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public EvidencedStringType getFullName() {
+            return fullName;
+        }
+
+        /**
+         * Sets the value of the fullName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public void setFullName(EvidencedStringType value) {
+            this.fullName = value;
+        }
+
+        /**
+         * Gets the value of the shortName property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the shortName property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getShortName().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List<EvidencedStringType> getShortName() {
+            if (shortName == null) {
+                shortName = new ArrayList<EvidencedStringType>();
+            }
+            return this.shortName;
+        }
+
+        /**
+         * Gets the value of the ecNumber property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the ecNumber property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getEcNumber().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List<EvidencedStringType> getEcNumber() {
+            if (ecNumber == null) {
+                ecNumber = new ArrayList<EvidencedStringType>();
+            }
+            return this.ecNumber;
+        }
 
-    /**
-     * Gets the value of the fullName property.
-     * 
-     * @return possible object is {@link EvidencedStringType }
-     * 
-     */
-    public EvidencedStringType getFullName()
-    {
-      return fullName;
     }
 
-    /**
-     * Sets the value of the fullName property.
-     * 
-     * @param value
-     *          allowed object is {@link EvidencedStringType }
-     * 
-     */
-    public void setFullName(EvidencedStringType value)
-    {
-      this.fullName = value;
-    }
 
     /**
-     * Gets the value of the ecNumber property.
+     * <p>Java class for anonymous complex type.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the ecNumber property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * <p>The following schema fragment specifies the expected content contained within this class.
      * 
      * <pre>
-     * getEcNumber().add(newItem);
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
+     *         &lt;element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+     *       &lt;/sequence>
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
      * </pre>
      * 
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
-     * 
-     * 
      */
-    public List<EvidencedStringType> getEcNumber()
-    {
-      if (ecNumber == null)
-      {
-        ecNumber = new ArrayList<EvidencedStringType>();
-      }
-      return this.ecNumber;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "fullName",
+        "ecNumber"
+    })
+    public static class SubmittedName {
+
+        @XmlElement(required = true)
+        protected EvidencedStringType fullName;
+        protected List<EvidencedStringType> ecNumber;
+
+        /**
+         * Gets the value of the fullName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public EvidencedStringType getFullName() {
+            return fullName;
+        }
+
+        /**
+         * Sets the value of the fullName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public void setFullName(EvidencedStringType value) {
+            this.fullName = value;
+        }
+
+        /**
+         * Gets the value of the ecNumber property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the ecNumber property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getEcNumber().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List<EvidencedStringType> getEcNumber() {
+            if (ecNumber == null) {
+                ecNumber = new ArrayList<EvidencedStringType>();
+            }
+            return this.ecNumber;
+        }
 
-  }
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/ReactionType.java b/src/jalview/xml/binding/uniprot/ReactionType.java
index bc660fe..0e84d09 100644
--- a/src/jalview/xml/binding/uniprot/ReactionType.java
+++ b/src/jalview/xml/binding/uniprot/ReactionType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,15 +16,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
  * Describes a chemical reaction.
  * 
- * <p>
- * Java class for reactionType complex type.
+ * <p>Java class for reactionType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="reactionType">
@@ -42,103 +41,99 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "reactionType", propOrder = { "text", "dbReference" })
-public class ReactionType
-{
-
-  @XmlElement(required = true)
-  protected String text;
+@XmlType(name = "reactionType", propOrder = {
+    "text",
+    "dbReference"
+})
+public class ReactionType {
 
-  @XmlElement(required = true)
-  protected List<DbReferenceType> dbReference;
+    @XmlElement(required = true)
+    protected String text;
+    @XmlElement(required = true)
+    protected List<DbReferenceType> dbReference;
+    @XmlAttribute(name = "evidence")
+    protected List<Integer> evidence;
 
-  @XmlAttribute(name = "evidence")
-  protected List<Integer> evidence;
-
-  /**
-   * Gets the value of the text property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getText()
-  {
-    return text;
-  }
+    /**
+     * Gets the value of the text property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getText() {
+        return text;
+    }
 
-  /**
-   * Sets the value of the text property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setText(String value)
-  {
-    this.text = value;
-  }
+    /**
+     * Sets the value of the text property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setText(String value) {
+        this.text = value;
+    }
 
-  /**
-   * Gets the value of the dbReference property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the dbReference property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getDbReference().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link DbReferenceType }
-   * 
-   * 
-   */
-  public List<DbReferenceType> getDbReference()
-  {
-    if (dbReference == null)
-    {
-      dbReference = new ArrayList<DbReferenceType>();
+    /**
+     * Gets the value of the dbReference property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the dbReference property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getDbReference().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link DbReferenceType }
+     * 
+     * 
+     */
+    public List<DbReferenceType> getDbReference() {
+        if (dbReference == null) {
+            dbReference = new ArrayList<DbReferenceType>();
+        }
+        return this.dbReference;
     }
-    return this.dbReference;
-  }
 
-  /**
-   * Gets the value of the evidence property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the evidence property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getEvidence().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List<Integer> getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList<Integer>();
+    /**
+     * Gets the value of the evidence property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the evidence property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getEvidence().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link Integer }
+     * 
+     * 
+     */
+    public List<Integer> getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList<Integer>();
+        }
+        return this.evidence;
     }
-    return this.evidence;
-  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/ReferenceType.java b/src/jalview/xml/binding/uniprot/ReferenceType.java
index 729acae..afd4647 100644
--- a/src/jalview/xml/binding/uniprot/ReferenceType.java
+++ b/src/jalview/xml/binding/uniprot/ReferenceType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,16 +16,14 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes a citation and a summary of its content. Equivalent to the flat
- * file RN-, RP-, RC-, RX-, RG-, RA-, RT- and RL-lines.
+ * Describes a citation and a summary of its content.
+ *             Equivalent to the flat file RN-, RP-, RC-, RX-, RG-, RA-, RT- and RL-lines.
  * 
- * <p>
- * Java class for referenceType complex type.
+ * <p>Java class for referenceType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="referenceType">
@@ -44,156 +43,151 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "referenceType",
-  propOrder =
-  { "citation", "scope", "source" })
-public class ReferenceType
-{
-
-  @XmlElement(required = true)
-  protected CitationType citation;
-
-  @XmlElement(required = true)
-  protected List<String> scope;
-
-  protected SourceDataType source;
-
-  @XmlAttribute(name = "evidence")
-  protected List<Integer> evidence;
-
-  @XmlAttribute(name = "key", required = true)
-  protected String key;
-
-  /**
-   * Gets the value of the citation property.
-   * 
-   * @return possible object is {@link CitationType }
-   * 
-   */
-  public CitationType getCitation()
-  {
-    return citation;
-  }
+@XmlType(name = "referenceType", propOrder = {
+    "citation",
+    "scope",
+    "source"
+})
+public class ReferenceType {
+
+    @XmlElement(required = true)
+    protected CitationType citation;
+    @XmlElement(required = true)
+    protected List<String> scope;
+    protected SourceDataType source;
+    @XmlAttribute(name = "evidence")
+    protected List<Integer> evidence;
+    @XmlAttribute(name = "key", required = true)
+    protected String key;
+
+    /**
+     * Gets the value of the citation property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link CitationType }
+     *     
+     */
+    public CitationType getCitation() {
+        return citation;
+    }
 
-  /**
-   * Sets the value of the citation property.
-   * 
-   * @param value
-   *          allowed object is {@link CitationType }
-   * 
-   */
-  public void setCitation(CitationType value)
-  {
-    this.citation = value;
-  }
+    /**
+     * Sets the value of the citation property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link CitationType }
+     *     
+     */
+    public void setCitation(CitationType value) {
+        this.citation = value;
+    }
 
-  /**
-   * Gets the value of the scope property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the scope property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getScope().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link String }
-   * 
-   * 
-   */
-  public List<String> getScope()
-  {
-    if (scope == null)
-    {
-      scope = new ArrayList<String>();
+    /**
+     * Gets the value of the scope property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the scope property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getScope().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
+     * 
+     */
+    public List<String> getScope() {
+        if (scope == null) {
+            scope = new ArrayList<String>();
+        }
+        return this.scope;
     }
-    return this.scope;
-  }
 
-  /**
-   * Gets the value of the source property.
-   * 
-   * @return possible object is {@link SourceDataType }
-   * 
-   */
-  public SourceDataType getSource()
-  {
-    return source;
-  }
+    /**
+     * Gets the value of the source property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link SourceDataType }
+     *     
+     */
+    public SourceDataType getSource() {
+        return source;
+    }
 
-  /**
-   * Sets the value of the source property.
-   * 
-   * @param value
-   *          allowed object is {@link SourceDataType }
-   * 
-   */
-  public void setSource(SourceDataType value)
-  {
-    this.source = value;
-  }
+    /**
+     * Sets the value of the source property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link SourceDataType }
+     *     
+     */
+    public void setSource(SourceDataType value) {
+        this.source = value;
+    }
 
-  /**
-   * Gets the value of the evidence property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the evidence property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getEvidence().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List<Integer> getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList<Integer>();
+    /**
+     * Gets the value of the evidence property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the evidence property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getEvidence().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link Integer }
+     * 
+     * 
+     */
+    public List<Integer> getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList<Integer>();
+        }
+        return this.evidence;
     }
-    return this.evidence;
-  }
 
-  /**
-   * Gets the value of the key property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getKey()
-  {
-    return key;
-  }
+    /**
+     * Gets the value of the key property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getKey() {
+        return key;
+    }
 
-  /**
-   * Sets the value of the key property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setKey(String value)
-  {
-    this.key = value;
-  }
+    /**
+     * Sets the value of the key property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setKey(String value) {
+        this.key = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/SequenceType.java b/src/jalview/xml/binding/uniprot/SequenceType.java
index 78ddd89..cddff7f 100644
--- a/src/jalview/xml/binding/uniprot/SequenceType.java
+++ b/src/jalview/xml/binding/uniprot/SequenceType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -15,13 +16,11 @@ import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 import javax.xml.datatype.XMLGregorianCalendar;
 
+
 /**
- * <p>
- * Java class for sequenceType complex type.
+ * <p>Java class for sequenceType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="sequenceType">
@@ -49,202 +48,195 @@ import javax.xml.datatype.XMLGregorianCalendar;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "sequenceType", propOrder = { "value" })
-public class SequenceType
-{
-
-  @XmlValue
-  protected String value;
-
-  @XmlAttribute(name = "length", required = true)
-  protected int length;
-
-  @XmlAttribute(name = "mass", required = true)
-  protected int mass;
-
-  @XmlAttribute(name = "checksum", required = true)
-  protected String checksum;
-
-  @XmlAttribute(name = "modified", required = true)
-  @XmlSchemaType(name = "date")
-  protected XMLGregorianCalendar modified;
-
-  @XmlAttribute(name = "version", required = true)
-  protected int version;
-
-  @XmlAttribute(name = "precursor")
-  protected Boolean precursor;
-
-  @XmlAttribute(name = "fragment")
-  protected String fragment;
-
-  /**
-   * Gets the value of the value property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getValue()
-  {
-    return value;
-  }
-
-  /**
-   * Sets the value of the value property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setValue(String value)
-  {
-    this.value = value;
-  }
-
-  /**
-   * Gets the value of the length property.
-   * 
-   */
-  public int getLength()
-  {
-    return length;
-  }
-
-  /**
-   * Sets the value of the length property.
-   * 
-   */
-  public void setLength(int value)
-  {
-    this.length = value;
-  }
-
-  /**
-   * Gets the value of the mass property.
-   * 
-   */
-  public int getMass()
-  {
-    return mass;
-  }
-
-  /**
-   * Sets the value of the mass property.
-   * 
-   */
-  public void setMass(int value)
-  {
-    this.mass = value;
-  }
-
-  /**
-   * Gets the value of the checksum property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getChecksum()
-  {
-    return checksum;
-  }
-
-  /**
-   * Sets the value of the checksum property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setChecksum(String value)
-  {
-    this.checksum = value;
-  }
-
-  /**
-   * Gets the value of the modified property.
-   * 
-   * @return possible object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public XMLGregorianCalendar getModified()
-  {
-    return modified;
-  }
-
-  /**
-   * Sets the value of the modified property.
-   * 
-   * @param value
-   *          allowed object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public void setModified(XMLGregorianCalendar value)
-  {
-    this.modified = value;
-  }
-
-  /**
-   * Gets the value of the version property.
-   * 
-   */
-  public int getVersion()
-  {
-    return version;
-  }
-
-  /**
-   * Sets the value of the version property.
-   * 
-   */
-  public void setVersion(int value)
-  {
-    this.version = value;
-  }
-
-  /**
-   * Gets the value of the precursor property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public Boolean isPrecursor()
-  {
-    return precursor;
-  }
-
-  /**
-   * Sets the value of the precursor property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setPrecursor(Boolean value)
-  {
-    this.precursor = value;
-  }
-
-  /**
-   * Gets the value of the fragment property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getFragment()
-  {
-    return fragment;
-  }
-
-  /**
-   * Sets the value of the fragment property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setFragment(String value)
-  {
-    this.fragment = value;
-  }
+@XmlType(name = "sequenceType", propOrder = {
+    "value"
+})
+public class SequenceType {
+
+    @XmlValue
+    protected String value;
+    @XmlAttribute(name = "length", required = true)
+    protected int length;
+    @XmlAttribute(name = "mass", required = true)
+    protected int mass;
+    @XmlAttribute(name = "checksum", required = true)
+    protected String checksum;
+    @XmlAttribute(name = "modified", required = true)
+    @XmlSchemaType(name = "date")
+    protected XMLGregorianCalendar modified;
+    @XmlAttribute(name = "version", required = true)
+    protected int version;
+    @XmlAttribute(name = "precursor")
+    protected Boolean precursor;
+    @XmlAttribute(name = "fragment")
+    protected String fragment;
+
+    /**
+     * Gets the value of the value property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getValue() {
+        return value;
+    }
+
+    /**
+     * Sets the value of the value property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setValue(String value) {
+        this.value = value;
+    }
+
+    /**
+     * Gets the value of the length property.
+     * 
+     */
+    public int getLength() {
+        return length;
+    }
+
+    /**
+     * Sets the value of the length property.
+     * 
+     */
+    public void setLength(int value) {
+        this.length = value;
+    }
+
+    /**
+     * Gets the value of the mass property.
+     * 
+     */
+    public int getMass() {
+        return mass;
+    }
+
+    /**
+     * Sets the value of the mass property.
+     * 
+     */
+    public void setMass(int value) {
+        this.mass = value;
+    }
+
+    /**
+     * Gets the value of the checksum property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getChecksum() {
+        return checksum;
+    }
+
+    /**
+     * Sets the value of the checksum property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setChecksum(String value) {
+        this.checksum = value;
+    }
+
+    /**
+     * Gets the value of the modified property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link XMLGregorianCalendar }
+     *     
+     */
+    public XMLGregorianCalendar getModified() {
+        return modified;
+    }
+
+    /**
+     * Sets the value of the modified property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link XMLGregorianCalendar }
+     *     
+     */
+    public void setModified(XMLGregorianCalendar value) {
+        this.modified = value;
+    }
+
+    /**
+     * Gets the value of the version property.
+     * 
+     */
+    public int getVersion() {
+        return version;
+    }
+
+    /**
+     * Sets the value of the version property.
+     * 
+     */
+    public void setVersion(int value) {
+        this.version = value;
+    }
+
+    /**
+     * Gets the value of the precursor property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public Boolean isPrecursor() {
+        return precursor;
+    }
+
+    /**
+     * Sets the value of the precursor property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setPrecursor(Boolean value) {
+        this.precursor = value;
+    }
+
+    /**
+     * Gets the value of the fragment property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getFragment() {
+        return fragment;
+    }
+
+    /**
+     * Sets the value of the fragment property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setFragment(String value) {
+        this.fragment = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/SourceDataType.java b/src/jalview/xml/binding/uniprot/SourceDataType.java
index 3b71bae..f66020c 100644
--- a/src/jalview/xml/binding/uniprot/SourceDataType.java
+++ b/src/jalview/xml/binding/uniprot/SourceDataType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -17,16 +18,14 @@ import javax.xml.bind.annotation.XmlElements;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
+
 /**
- * Describes the source of the sequence according to the citation. Equivalent to
- * the flat file RC-line.
+ * Describes the source of the sequence according to the citation.
+ *             Equivalent to the flat file RC-line.
  * 
- * <p>
- * Java class for sourceDataType complex type.
+ * <p>Java class for sourceDataType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="sourceDataType">
@@ -78,401 +77,385 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "sourceDataType",
-  propOrder =
-  { "strainOrPlasmidOrTransposon" })
-public class SourceDataType
-{
-
-  @XmlElements({
-      @XmlElement(name = "strain", type = SourceDataType.Strain.class),
-      @XmlElement(name = "plasmid", type = SourceDataType.Plasmid.class),
-      @XmlElement(
-        name = "transposon",
-        type = SourceDataType.Transposon.class),
-      @XmlElement(name = "tissue", type = SourceDataType.Tissue.class) })
-  protected List<Object> strainOrPlasmidOrTransposon;
-
-  /**
-   * Gets the value of the strainOrPlasmidOrTransposon property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the strainOrPlasmidOrTransposon property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getStrainOrPlasmidOrTransposon().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link SourceDataType.Strain } {@link SourceDataType.Plasmid }
-   * {@link SourceDataType.Transposon } {@link SourceDataType.Tissue }
-   * 
-   * 
-   */
-  public List<Object> getStrainOrPlasmidOrTransposon()
-  {
-    if (strainOrPlasmidOrTransposon == null)
-    {
-      strainOrPlasmidOrTransposon = new ArrayList<Object>();
-    }
-    return this.strainOrPlasmidOrTransposon;
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;simpleContent>
-   *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
-   *       &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-   *     &lt;/extension>
-   *   &lt;/simpleContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "value" })
-  public static class Plasmid
-  {
-
-    @XmlValue
-    protected String value;
-
-    @XmlAttribute(name = "evidence")
-    protected List<Integer> evidence;
-
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getValue()
-    {
-      return value;
-    }
+@XmlType(name = "sourceDataType", propOrder = {
+    "strainOrPlasmidOrTransposon"
+})
+public class SourceDataType {
+
+    @XmlElements({
+        @XmlElement(name = "strain", type = SourceDataType.Strain.class),
+        @XmlElement(name = "plasmid", type = SourceDataType.Plasmid.class),
+        @XmlElement(name = "transposon", type = SourceDataType.Transposon.class),
+        @XmlElement(name = "tissue", type = SourceDataType.Tissue.class)
+    })
+    protected List<Object> strainOrPlasmidOrTransposon;
 
     /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setValue(String value)
-    {
-      this.value = value;
-    }
-
-    /**
-     * Gets the value of the evidence property.
+     * Gets the value of the strainOrPlasmidOrTransposon property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the evidence property.
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the strainOrPlasmidOrTransposon property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
-     * 
      * <pre>
-     * getEvidence().add(newItem);
+     *    getStrainOrPlasmidOrTransposon().add(newItem);
      * </pre>
      * 
      * 
      * <p>
-     * Objects of the following type(s) are allowed in the list {@link Integer }
+     * Objects of the following type(s) are allowed in the list
+     * {@link SourceDataType.Strain }
+     * {@link SourceDataType.Plasmid }
+     * {@link SourceDataType.Transposon }
+     * {@link SourceDataType.Tissue }
      * 
      * 
      */
-    public List<Integer> getEvidence()
-    {
-      if (evidence == null)
-      {
-        evidence = new ArrayList<Integer>();
-      }
-      return this.evidence;
+    public List<Object> getStrainOrPlasmidOrTransposon() {
+        if (strainOrPlasmidOrTransposon == null) {
+            strainOrPlasmidOrTransposon = new ArrayList<Object>();
+        }
+        return this.strainOrPlasmidOrTransposon;
     }
 
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;simpleContent>
-   *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
-   *       &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-   *     &lt;/extension>
-   *   &lt;/simpleContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "value" })
-  public static class Strain
-  {
-
-    @XmlValue
-    protected String value;
-
-    @XmlAttribute(name = "evidence")
-    protected List<Integer> evidence;
 
     /**
-     * Gets the value of the value property.
+     * <p>Java class for anonymous complex type.
      * 
-     * @return possible object is {@link String }
+     * <p>The following schema fragment specifies the expected content contained within this class.
      * 
-     */
-    public String getValue()
-    {
-      return value;
-    }
-
-    /**
-     * Sets the value of the value property.
+     * <pre>
+     * &lt;complexType>
+     *   &lt;simpleContent>
+     *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
+     *       &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+     *     &lt;/extension>
+     *   &lt;/simpleContent>
+     * &lt;/complexType>
+     * </pre>
      * 
-     * @param value
-     *          allowed object is {@link String }
      * 
      */
-    public void setValue(String value)
-    {
-      this.value = value;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "value"
+    })
+    public static class Plasmid {
+
+        @XmlValue
+        protected String value;
+        @XmlAttribute(name = "evidence")
+        protected List<Integer> evidence;
+
+        /**
+         * Gets the value of the value property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getValue() {
+            return value;
+        }
+
+        /**
+         * Sets the value of the value property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setValue(String value) {
+            this.value = value;
+        }
+
+        /**
+         * Gets the value of the evidence property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the evidence property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getEvidence().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link Integer }
+         * 
+         * 
+         */
+        public List<Integer> getEvidence() {
+            if (evidence == null) {
+                evidence = new ArrayList<Integer>();
+            }
+            return this.evidence;
+        }
+
     }
 
+
     /**
-     * Gets the value of the evidence property.
+     * <p>Java class for anonymous complex type.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the evidence property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * <p>The following schema fragment specifies the expected content contained within this class.
      * 
      * <pre>
-     * getEvidence().add(newItem);
+     * &lt;complexType>
+     *   &lt;simpleContent>
+     *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
+     *       &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+     *     &lt;/extension>
+     *   &lt;/simpleContent>
+     * &lt;/complexType>
      * </pre>
      * 
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list {@link Integer }
-     * 
-     * 
      */
-    public List<Integer> getEvidence()
-    {
-      if (evidence == null)
-      {
-        evidence = new ArrayList<Integer>();
-      }
-      return this.evidence;
-    }
-
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;simpleContent>
-   *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
-   *       &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-   *     &lt;/extension>
-   *   &lt;/simpleContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "value" })
-  public static class Tissue
-  {
-
-    @XmlValue
-    protected String value;
-
-    @XmlAttribute(name = "evidence")
-    protected List<Integer> evidence;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "value"
+    })
+    public static class Strain {
+
+        @XmlValue
+        protected String value;
+        @XmlAttribute(name = "evidence")
+        protected List<Integer> evidence;
+
+        /**
+         * Gets the value of the value property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getValue() {
+            return value;
+        }
+
+        /**
+         * Sets the value of the value property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setValue(String value) {
+            this.value = value;
+        }
+
+        /**
+         * Gets the value of the evidence property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the evidence property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getEvidence().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link Integer }
+         * 
+         * 
+         */
+        public List<Integer> getEvidence() {
+            if (evidence == null) {
+                evidence = new ArrayList<Integer>();
+            }
+            return this.evidence;
+        }
 
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getValue()
-    {
-      return value;
     }
 
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setValue(String value)
-    {
-      this.value = value;
-    }
 
     /**
-     * Gets the value of the evidence property.
+     * <p>Java class for anonymous complex type.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the evidence property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * <p>The following schema fragment specifies the expected content contained within this class.
      * 
      * <pre>
-     * getEvidence().add(newItem);
+     * &lt;complexType>
+     *   &lt;simpleContent>
+     *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
+     *       &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+     *     &lt;/extension>
+     *   &lt;/simpleContent>
+     * &lt;/complexType>
      * </pre>
      * 
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list {@link Integer }
-     * 
-     * 
      */
-    public List<Integer> getEvidence()
-    {
-      if (evidence == null)
-      {
-        evidence = new ArrayList<Integer>();
-      }
-      return this.evidence;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "value"
+    })
+    public static class Tissue {
+
+        @XmlValue
+        protected String value;
+        @XmlAttribute(name = "evidence")
+        protected List<Integer> evidence;
+
+        /**
+         * Gets the value of the value property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getValue() {
+            return value;
+        }
+
+        /**
+         * Sets the value of the value property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setValue(String value) {
+            this.value = value;
+        }
+
+        /**
+         * Gets the value of the evidence property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the evidence property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getEvidence().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link Integer }
+         * 
+         * 
+         */
+        public List<Integer> getEvidence() {
+            if (evidence == null) {
+                evidence = new ArrayList<Integer>();
+            }
+            return this.evidence;
+        }
 
-  }
-
-  /**
-   * <p>
-   * Java class for anonymous complex type.
-   * 
-   * <p>
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * <pre>
-   * &lt;complexType>
-   *   &lt;simpleContent>
-   *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
-   *       &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-   *     &lt;/extension>
-   *   &lt;/simpleContent>
-   * &lt;/complexType>
-   * </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "value" })
-  public static class Transposon
-  {
-
-    @XmlValue
-    protected String value;
-
-    @XmlAttribute(name = "evidence")
-    protected List<Integer> evidence;
-
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getValue()
-    {
-      return value;
     }
 
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setValue(String value)
-    {
-      this.value = value;
-    }
 
     /**
-     * Gets the value of the evidence property.
+     * <p>Java class for anonymous complex type.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
-     * be present inside the JAXB object. This is why there is not a
-     * <CODE>set</CODE> method for the evidence property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * <p>The following schema fragment specifies the expected content contained within this class.
      * 
      * <pre>
-     * getEvidence().add(newItem);
+     * &lt;complexType>
+     *   &lt;simpleContent>
+     *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
+     *       &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+     *     &lt;/extension>
+     *   &lt;/simpleContent>
+     * &lt;/complexType>
      * </pre>
      * 
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list {@link Integer }
-     * 
-     * 
      */
-    public List<Integer> getEvidence()
-    {
-      if (evidence == null)
-      {
-        evidence = new ArrayList<Integer>();
-      }
-      return this.evidence;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "value"
+    })
+    public static class Transposon {
+
+        @XmlValue
+        protected String value;
+        @XmlAttribute(name = "evidence")
+        protected List<Integer> evidence;
+
+        /**
+         * Gets the value of the value property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getValue() {
+            return value;
+        }
+
+        /**
+         * Sets the value of the value property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setValue(String value) {
+            this.value = value;
+        }
+
+        /**
+         * Gets the value of the evidence property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the evidence property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getEvidence().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link Integer }
+         * 
+         * 
+         */
+        public List<Integer> getEvidence() {
+            if (evidence == null) {
+                evidence = new ArrayList<Integer>();
+            }
+            return this.evidence;
+        }
 
-  }
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/SourceType.java b/src/jalview/xml/binding/uniprot/SourceType.java
index 5d71178..012d588 100644
--- a/src/jalview/xml/binding/uniprot/SourceType.java
+++ b/src/jalview/xml/binding/uniprot/SourceType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.math.BigInteger;
@@ -13,17 +14,13 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes the source of the data using a database cross-reference (or a 'ref'
- * attribute when the source cannot be found in a public data source, such as
- * PubMed, and is cited only within the UniProtKB entry).
+ * Describes the source of the data using a database cross-reference (or a 'ref' attribute when the source cannot be found in a public data source, such as PubMed, and is cited only within the UniProtKB entry).
  * 
- * <p>
- * Java class for sourceType complex type.
+ * <p>Java class for sourceType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="sourceType">
@@ -41,59 +38,61 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "sourceType", propOrder = { "dbReference" })
-public class SourceType
-{
-
-  protected DbReferenceType dbReference;
+@XmlType(name = "sourceType", propOrder = {
+    "dbReference"
+})
+public class SourceType {
 
-  @XmlAttribute(name = "ref")
-  protected BigInteger ref;
+    protected DbReferenceType dbReference;
+    @XmlAttribute(name = "ref")
+    protected BigInteger ref;
 
-  /**
-   * Gets the value of the dbReference property.
-   * 
-   * @return possible object is {@link DbReferenceType }
-   * 
-   */
-  public DbReferenceType getDbReference()
-  {
-    return dbReference;
-  }
+    /**
+     * Gets the value of the dbReference property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link DbReferenceType }
+     *     
+     */
+    public DbReferenceType getDbReference() {
+        return dbReference;
+    }
 
-  /**
-   * Sets the value of the dbReference property.
-   * 
-   * @param value
-   *          allowed object is {@link DbReferenceType }
-   * 
-   */
-  public void setDbReference(DbReferenceType value)
-  {
-    this.dbReference = value;
-  }
+    /**
+     * Sets the value of the dbReference property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link DbReferenceType }
+     *     
+     */
+    public void setDbReference(DbReferenceType value) {
+        this.dbReference = value;
+    }
 
-  /**
-   * Gets the value of the ref property.
-   * 
-   * @return possible object is {@link BigInteger }
-   * 
-   */
-  public BigInteger getRef()
-  {
-    return ref;
-  }
+    /**
+     * Gets the value of the ref property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link BigInteger }
+     *     
+     */
+    public BigInteger getRef() {
+        return ref;
+    }
 
-  /**
-   * Sets the value of the ref property.
-   * 
-   * @param value
-   *          allowed object is {@link BigInteger }
-   * 
-   */
-  public void setRef(BigInteger value)
-  {
-    this.ref = value;
-  }
+    /**
+     * Sets the value of the ref property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link BigInteger }
+     *     
+     */
+    public void setRef(BigInteger value) {
+        this.ref = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/StatusType.java b/src/jalview/xml/binding/uniprot/StatusType.java
index 5f22a99..8411265 100644
--- a/src/jalview/xml/binding/uniprot/StatusType.java
+++ b/src/jalview/xml/binding/uniprot/StatusType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,15 +14,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
+
 /**
  * Indicates whether the name of a plasmid is known or unknown.
  * 
- * <p>
- * Java class for statusType complex type.
+ * <p>Java class for statusType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="statusType">
@@ -43,67 +42,66 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "statusType", propOrder = { "value" })
-public class StatusType
-{
-
-  @XmlValue
-  protected String value;
-
-  @XmlAttribute(name = "status")
-  protected String status;
+@XmlType(name = "statusType", propOrder = {
+    "value"
+})
+public class StatusType {
 
-  /**
-   * Gets the value of the value property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getValue()
-  {
-    return value;
-  }
+    @XmlValue
+    protected String value;
+    @XmlAttribute(name = "status")
+    protected String status;
 
-  /**
-   * Sets the value of the value property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setValue(String value)
-  {
-    this.value = value;
-  }
+    /**
+     * Gets the value of the value property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getValue() {
+        return value;
+    }
 
-  /**
-   * Gets the value of the status property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getStatus()
-  {
-    if (status == null)
-    {
-      return "known";
+    /**
+     * Sets the value of the value property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setValue(String value) {
+        this.value = value;
     }
-    else
-    {
-      return status;
+
+    /**
+     * Gets the value of the status property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getStatus() {
+        if (status == null) {
+            return "known";
+        } else {
+            return status;
+        }
     }
-  }
 
-  /**
-   * Sets the value of the status property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setStatus(String value)
-  {
-    this.status = value;
-  }
+    /**
+     * Sets the value of the status property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setStatus(String value) {
+        this.status = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/SubcellularLocationType.java b/src/jalview/xml/binding/uniprot/SubcellularLocationType.java
index f1a06ef..77765a7 100644
--- a/src/jalview/xml/binding/uniprot/SubcellularLocationType.java
+++ b/src/jalview/xml/binding/uniprot/SubcellularLocationType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -14,16 +15,13 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes the subcellular location and optionally the topology and
- * orientation of a molecule.
+ * Describes the subcellular location and optionally the topology and orientation of a molecule.
  * 
- * <p>
- * Java class for subcellularLocationType complex type.
+ * <p>Java class for subcellularLocationType complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType name="subcellularLocationType">
@@ -42,114 +40,103 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "subcellularLocationType",
-  propOrder =
-  { "location", "topology", "orientation" })
-public class SubcellularLocationType
-{
-
-  @XmlElement(required = true)
-  protected List<EvidencedStringType> location;
-
-  protected List<EvidencedStringType> topology;
+@XmlType(name = "subcellularLocationType", propOrder = {
+    "location",
+    "topology",
+    "orientation"
+})
+public class SubcellularLocationType {
 
-  protected List<EvidencedStringType> orientation;
+    @XmlElement(required = true)
+    protected List<EvidencedStringType> location;
+    protected List<EvidencedStringType> topology;
+    protected List<EvidencedStringType> orientation;
 
-  /**
-   * Gets the value of the location property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the location property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getLocation().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link EvidencedStringType }
-   * 
-   * 
-   */
-  public List<EvidencedStringType> getLocation()
-  {
-    if (location == null)
-    {
-      location = new ArrayList<EvidencedStringType>();
+    /**
+     * Gets the value of the location property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the location property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getLocation().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link EvidencedStringType }
+     * 
+     * 
+     */
+    public List<EvidencedStringType> getLocation() {
+        if (location == null) {
+            location = new ArrayList<EvidencedStringType>();
+        }
+        return this.location;
     }
-    return this.location;
-  }
 
-  /**
-   * Gets the value of the topology property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the topology property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getTopology().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link EvidencedStringType }
-   * 
-   * 
-   */
-  public List<EvidencedStringType> getTopology()
-  {
-    if (topology == null)
-    {
-      topology = new ArrayList<EvidencedStringType>();
+    /**
+     * Gets the value of the topology property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the topology property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getTopology().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link EvidencedStringType }
+     * 
+     * 
+     */
+    public List<EvidencedStringType> getTopology() {
+        if (topology == null) {
+            topology = new ArrayList<EvidencedStringType>();
+        }
+        return this.topology;
     }
-    return this.topology;
-  }
 
-  /**
-   * Gets the value of the orientation property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the orientation property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getOrientation().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
-   * {@link EvidencedStringType }
-   * 
-   * 
-   */
-  public List<EvidencedStringType> getOrientation()
-  {
-    if (orientation == null)
-    {
-      orientation = new ArrayList<EvidencedStringType>();
+    /**
+     * Gets the value of the orientation property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the orientation property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getOrientation().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link EvidencedStringType }
+     * 
+     * 
+     */
+    public List<EvidencedStringType> getOrientation() {
+        if (orientation == null) {
+            orientation = new ArrayList<EvidencedStringType>();
+        }
+        return this.orientation;
     }
-    return this.orientation;
-  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/Uniprot.java b/src/jalview/xml/binding/uniprot/Uniprot.java
index 3383e5d..a18d58b 100644
--- a/src/jalview/xml/binding/uniprot/Uniprot.java
+++ b/src/jalview/xml/binding/uniprot/Uniprot.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,13 +16,11 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>
- * Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
  * 
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
  * <pre>
  * &lt;complexType>
@@ -39,68 +38,68 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = { "entry", "copyright" })
+@XmlType(name = "", propOrder = {
+    "entry",
+    "copyright"
+})
 @XmlRootElement(name = "uniprot")
-public class Uniprot
-{
-
-  @XmlElement(required = true)
-  protected List<Entry> entry;
+public class Uniprot {
 
-  protected String copyright;
+    @XmlElement(required = true)
+    protected List<Entry> entry;
+    protected String copyright;
 
-  /**
-   * Gets the value of the entry property.
-   * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the entry property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
-   * 
-   * <pre>
-   * getEntry().add(newItem);
-   * </pre>
-   * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list {@link Entry }
-   * 
-   * 
-   */
-  public List<Entry> getEntry()
-  {
-    if (entry == null)
-    {
-      entry = new ArrayList<Entry>();
+    /**
+     * Gets the value of the entry property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the entry property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getEntry().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link Entry }
+     * 
+     * 
+     */
+    public List<Entry> getEntry() {
+        if (entry == null) {
+            entry = new ArrayList<Entry>();
+        }
+        return this.entry;
     }
-    return this.entry;
-  }
 
-  /**
-   * Gets the value of the copyright property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getCopyright()
-  {
-    return copyright;
-  }
+    /**
+     * Gets the value of the copyright property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getCopyright() {
+        return copyright;
+    }
 
-  /**
-   * Sets the value of the copyright property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setCopyright(String value)
-  {
-    this.copyright = value;
-  }
+    /**
+     * Sets the value of the copyright property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setCopyright(String value) {
+        this.copyright = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/package-info.java b/src/jalview/xml/binding/uniprot/package-info.java
index 8a7c699..b8a8636 100644
--- a/src/jalview/xml/binding/uniprot/package-info.java
+++ b/src/jalview/xml/binding/uniprot/package-info.java
@@ -2,10 +2,8 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
-@javax.xml.bind.annotation.XmlSchema(
-  namespace = "http://uniprot.org/uniprot",
-  elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
+@javax.xml.bind.annotation.XmlSchema(namespace = "http://uniprot.org/uniprot", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
 package jalview.xml.binding.uniprot;
diff --git a/test/jalview/gui/AlignmentPanelTest.java b/test/jalview/gui/AlignmentPanelTest.java
index a137ff6..2d7e3dc 100644
--- a/test/jalview/gui/AlignmentPanelTest.java
+++ b/test/jalview/gui/AlignmentPanelTest.java
@@ -22,6 +22,7 @@ package jalview.gui;
 
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertNotEquals;
+import static org.testng.Assert.assertNotNull;
 
 import java.awt.Dimension;
 import java.awt.Font;
@@ -290,4 +291,43 @@ public class AlignmentPanelTest
     Cache.setProperty("FIGURE_AUTOIDWIDTH", Boolean.TRUE.toString());
     assertEquals(115, af.alignPanel.getVisibleIdWidth(false));
   }
-}
+ 
+  @Test(groups = "Functional")
+  public void testSetOverviewTitle()
+  {
+    OverviewPanel ov1 = this.af.openOverviewPanel(true);
+    String alignFrameTitle = af.getTitle();
+    assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle);
+    
+    /*
+     * on New View, existing overview should get " Original" added to title
+     * and new view's overview should get " View 1" added
+     */
+    af.newView_actionPerformed(null);
+    assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle + " Original");
+    OverviewPanel ov2 = this.af.openOverviewPanel(true);
+    assertEquals(ov2.getTitle(), "Overview " + alignFrameTitle + " View 1");
+  }
+  
+  @Test(groups = "Functional")
+  public void testSetOverviewTitle_automaticOverview()
+  {
+    Cache.setProperty("SHOW_OVERVIEW",  "true");
+    AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", DataSourceType.FILE);
+    OverviewPanel ov1 = alignFrame.alignPanel.getOverviewPanel();
+    assertNotNull(ov1);
+    String alignFrameTitle = alignFrame.getTitle();
+    assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle);
+    
+    /*
+     * on New View, existing overview should get " Original" added to title
+     * and new view's automatic overview should have " View 1" added
+     */
+    alignFrame.newView_actionPerformed(null);
+    assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle + " Original");
+    OverviewPanel ov2 = alignFrame.alignPanel.getOverviewPanel();
+    assertNotNull(ov2);
+    assertEquals(ov2.getTitle(), "Overview " + alignFrameTitle + " View 1");
+  }
+}
\ No newline at end of file
diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 79d622c..23a8be6 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -23,11 +23,13 @@ package jalview.project;
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertNotSame;
 import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
 import java.awt.Color;
+import java.awt.Rectangle;
 import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
@@ -48,6 +50,7 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureColourI;
 import jalview.api.ViewStyleI;
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
@@ -69,8 +72,10 @@ import jalview.gui.AlignViewport;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
+import jalview.gui.OverviewPanel;
 import jalview.gui.PCAPanel;
 import jalview.gui.PopupMenu;
+import jalview.gui.Preferences;
 import jalview.gui.SliderPanel;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
@@ -1274,4 +1279,117 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     assertTrue(dbRef instanceof GeneLocus);
     assertEquals(dbRef, dbref3);
   }
+
+  /**
+   * test store and recovery of Overview windows
+   * 
+   * @throws Exception
+   */
+  @Test(groups = { "Functional" }, enabled = true)
+  public void testStoreAndRecoverOverview() throws Exception
+  {
+    Desktop.instance.closeAll_actionPerformed(null);
+
+    Cache.setProperty("SHOW_OVERVIEW", "false");
+    Cache.setProperty(Preferences.USE_LEGACY_GAP, "false");
+    Cache.setColourProperty(Preferences.GAP_COLOUR, Color.green);
+    Cache.setColourProperty(Preferences.HIDDEN_COLOUR, Color.yellow);
+    Cache.setProperty(Preferences.SHOW_OV_HIDDEN_AT_START, "true");
+
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", DataSourceType.FILE);
+
+    /*
+     * open and resize / reposition overview 
+     */
+    af.overviewMenuItem_actionPerformed(null);
+    OverviewPanel ov1 = af.alignPanel.getOverviewPanel();
+    assertNotNull(ov1);
+    ov1.setFrameBounds(20, 30, 200, 400);
+    assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa");
+    assertTrue(ov1.isShowHiddenRegions());
+
+    /*
+     * open a New View and its Overview and reposition it
+     */
+    af.newView_actionPerformed(null);
+    af.overviewMenuItem_actionPerformed(null);
+    OverviewPanel ov2 = af.alignPanel.getOverviewPanel();
+    assertNotNull(ov2);
+    assertNotSame(ov1, ov2);
+    ov2.setFrameBounds(25, 35, 205, 405);
+    assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa Original");
+    assertEquals(ov2.getTitle(), "Overview examples/uniref50.fa View 1");
+
+    File tfile = File.createTempFile("testStoreAndRecoverOverview", ".jvp");
+    new Jalview2XML(false).saveState(tfile);
+    Desktop.instance.closeAll_actionPerformed(null);
+
+    /*
+     * change preferences (should _not_ affect reloaded Overviews)
+     */
+    Cache.setProperty("SHOW_OVERVIEW", "true");
+    Cache.setProperty(Preferences.USE_LEGACY_GAP, "true");
+    Cache.setColourProperty(Preferences.GAP_COLOUR, Color.blue);
+    Cache.setColourProperty(Preferences.HIDDEN_COLOUR, Color.orange);
+    Cache.setProperty(Preferences.SHOW_OV_HIDDEN_AT_START, "false");
+
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+            DataSourceType.FILE);
+
+    /*
+     * workaround: explicitly select View 1 (not in focus after restore)
+     */
+    af.tabSelectionChanged(1);
+
+    /*
+     * verify restored overview for View 1
+     */
+    ov2 = af.alignPanel.getOverviewPanel();
+    assertEquals(ov2.getCanvas().getGapColour(), Color.green);
+    // 'non-legacy' colouring uses white for non-gapped residues
+    assertEquals(ov2.getCanvas().getResidueColour(), Color.white);
+    assertEquals(ov2.getCanvas().getHiddenColour(), Color.yellow);
+    assertEquals(ov2.getTitle(), "Overview examples/uniref50.fa View 1");
+    assertEquals(ov2.getFrameBounds(), new Rectangle(25, 35, 205, 405));
+    assertTrue(ov2.isShowHiddenRegions());
+
+    /*
+     * verify restored overview for Original view
+     */
+    af.tabSelectionChanged(0);
+    ov1 = af.alignPanel.getOverviewPanel();
+    assertEquals(ov1.getCanvas().getGapColour(), Color.green);
+    // 'non-legacy' colouring uses white for non-gapped residues
+    assertEquals(ov1.getCanvas().getResidueColour(), Color.white);
+    assertEquals(ov1.getCanvas().getHiddenColour(), Color.yellow);
+    assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa Original");
+    assertEquals(ov1.getFrameBounds(), new Rectangle(20, 30, 200, 400));
+    assertTrue(ov1.isShowHiddenRegions());
+  }
+
+  /**
+   * Test that a view with no Overview is restored with no Overview, even if
+   * 'Open Overview' is selected in Preferences
+   * 
+   * @throws Exception
+   */
+  @Test(groups = { "Functional" }, enabled = true)
+  public void testStoreAndRecoverNoOverview() throws Exception
+  {
+    Cache.setProperty("SHOW_OVERVIEW", "false");
+    Desktop.instance.closeAll_actionPerformed(null);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            ">seq1\nMATRSQFLVNF\n", DataSourceType.PASTE);
+
+    File tfile = File.createTempFile("testStoreAndRecoverOverview", ".jvp");
+    new Jalview2XML(false).saveState(tfile);
+    Desktop.instance.closeAll_actionPerformed(null);
+
+    Cache.setProperty("SHOW_OVERVIEW", "true");
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+            DataSourceType.FILE);
+
+    assertNull(af.alignPanel.getOverviewPanel());
+  }
 }
diff --git a/test/jalview/renderer/OverviewRendererTest.java b/test/jalview/renderer/OverviewRendererTest.java
index c59e520..cdb69e3 100644
--- a/test/jalview/renderer/OverviewRendererTest.java
+++ b/test/jalview/renderer/OverviewRendererTest.java
@@ -46,8 +46,9 @@ public class OverviewRendererTest
   @Test
   public void testGetColumnColourFromSequence()
   {
-    OverviewResColourFinder cf = new OverviewResColourFinder(false,
-            Color.PINK, Color.green); // gapColour, hiddenColour
+    // gapColour, residueColour, hiddenColour
+    OverviewResColourFinder cf = new OverviewResColourFinder(
+            Color.PINK, Color.white, Color.green); 
     Sequence seq1 = new Sequence("seq1", "PQ-RL-");
     Sequence seq2 = new Sequence("seq2", "FVE");
     AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
diff --git a/test/jalview/renderer/OverviewResColourFinderTest.java b/test/jalview/renderer/OverviewResColourFinderTest.java
index 3931dbf..028777e 100644
--- a/test/jalview/renderer/OverviewResColourFinderTest.java
+++ b/test/jalview/renderer/OverviewResColourFinderTest.java
@@ -22,6 +22,12 @@ package jalview.renderer;
 
 import static org.testng.AssertJUnit.assertEquals;
 
+import java.awt.Color;
+import java.util.ArrayList;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -30,16 +36,11 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignViewport;
 import jalview.gui.JvOptionPane;
+import jalview.gui.OverviewCanvas;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.UserColourScheme;
 import jalview.schemes.ZappoColourScheme;
 
-import java.awt.Color;
-import java.util.ArrayList;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
 public class OverviewResColourFinderTest
 {
 
@@ -185,7 +186,7 @@ public class OverviewResColourFinderTest
             av.getResidueShading(), groups, seq, 2, null));
 
     // use legacy colouring
-    rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
+    rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red);
 
     // G in group specified as magenta in Zappo
     assertEquals(Color.magenta, rcf.getResidueColour(false,
@@ -200,7 +201,7 @@ public class OverviewResColourFinderTest
             av.getResidueShading(), groups, seq, 2, null));
 
     // use new colouring
-    rcf = new OverviewResColourFinder(false, Color.blue, Color.red);
+    rcf = new OverviewResColourFinder(Color.blue, Color.white, Color.red);
 
     // G in group specified as magenta in Zappo
     assertEquals(Color.magenta, rcf.getResidueColour(false,
@@ -233,12 +234,10 @@ public class OverviewResColourFinderTest
 
     // gaps gap colour
     c = rcf.getBoxColour(shader, seq, 3);
-    assertEquals(
-            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP,
-            c);
+    assertEquals(OverviewCanvas.OVERVIEW_DEFAULT_GAP, c);
 
     // legacy colouring set explicitly via constructor
-    rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
+    rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red);
     shader = new ResidueShader();
 
     // residues light gray
@@ -259,12 +258,10 @@ public class OverviewResColourFinderTest
 
     // gaps gap colour
     c = rcf.getBoxColour(shader, seq, 3);
-    assertEquals(
-            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP,
-            c);
+    assertEquals(OverviewCanvas.OVERVIEW_DEFAULT_GAP, c);
 
     // non legacy colouring with colour scheme
-    rcf = new OverviewResColourFinder(false, Color.blue, Color.red);
+    rcf = new OverviewResColourFinder(Color.blue, Color.white, Color.red);
     shader = new ResidueShader(new ZappoColourScheme());
 
     // M residue pink
@@ -276,7 +273,7 @@ public class OverviewResColourFinderTest
     assertEquals(Color.blue, c);
 
     // legacy colouring with colour scheme
-    rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
+    rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red);
 
     // M residue pink
     c = rcf.getBoxColour(shader, seq, 0);