From c25cfde239527da78fecce55a877330afa90701d Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 20 Dec 2018 13:36:33 +0000
Subject: [PATCH] JAL-1767 port save/load PCA panel to JAXB - JAL-3063

---
 src/jalview/gui/Jalview2XML.java                   |   38 +-
 src/jalview/gui/PCAPanel.java                      |  137 +-
 src/jalview/gui/RotatableCanvas.java               |  108 +-
 src/jalview/gui/TreeCanvas.java                    |   10 +
 src/jalview/project/Jalview2XML.java               |  360 +++++
 src/jalview/xml/binding/jalview/AlcodonFrame.java  |    2 +-
 src/jalview/xml/binding/jalview/Annotation.java    |    2 +-
 .../binding/jalview/AnnotationColourScheme.java    |    2 +-
 .../xml/binding/jalview/AnnotationElement.java     |    2 +-
 src/jalview/xml/binding/jalview/DoubleMatrix.java  |  186 +++
 src/jalview/xml/binding/jalview/DoubleVector.java  |   76 +
 src/jalview/xml/binding/jalview/Feature.java       |    2 +-
 .../xml/binding/jalview/FeatureMatcher.java        |    2 +-
 .../xml/binding/jalview/FeatureMatcherSet.java     |    2 +-
 src/jalview/xml/binding/jalview/FilterBy.java      |    2 +-
 src/jalview/xml/binding/jalview/JalviewModel.java  | 1453 ++++++++++++++++++--
 .../xml/binding/jalview/JalviewUserColours.java    |    2 +-
 src/jalview/xml/binding/jalview/MapListType.java   |    2 +-
 src/jalview/xml/binding/jalview/Mapping.java       |    2 +-
 src/jalview/xml/binding/jalview/NoValueColour.java |    2 +-
 src/jalview/xml/binding/jalview/ObjectFactory.java |   66 +-
 src/jalview/xml/binding/jalview/PcaDataType.java   |  129 ++
 src/jalview/xml/binding/jalview/Pdbentry.java      |    2 +-
 src/jalview/xml/binding/jalview/Sequence.java      |    2 +-
 src/jalview/xml/binding/jalview/SequenceSet.java   |    2 +-
 src/jalview/xml/binding/jalview/SequenceType.java  |    2 +-
 src/jalview/xml/binding/jalview/ThresholdType.java |    2 +-
 src/jalview/xml/binding/jalview/VAMSAS.java        |    2 +-
 .../binding/jalview/WebServiceParameterSet.java    |    2 +-
 src/jalview/xml/binding/jalview/package-info.java  |    2 +-
 30 files changed, 2370 insertions(+), 233 deletions(-)
 create mode 100644 src/jalview/xml/binding/jalview/DoubleMatrix.java
 create mode 100644 src/jalview/xml/binding/jalview/DoubleVector.java
 create mode 100644 src/jalview/xml/binding/jalview/PcaDataType.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 7cfaa7d..7f07a20 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1570,27 +1570,27 @@ public class Jalview2XML
       viewer.setXpos(panel.getX());
       viewer.setYpos(panel.getY());
       viewer.setTitle(panel.getTitle());
-      PCAModel pcaModel = panel.pcaModel;
+      PCAModel pcaModel = panel.getPcaModel();
       viewer.setScoreModelName(pcaModel.getScoreModelName());
       viewer.setXDim(panel.getSelectedDimensionIndex(X));
       viewer.setYDim(panel.getSelectedDimensionIndex(Y));
       viewer.setZDim(panel.getSelectedDimensionIndex(Z));
-      viewer.setBgColour(panel.rc.getBackgroundColour().getRGB());
-      viewer.setScaleFactor(panel.rc.scaleFactor);
-      float[] spMin = panel.rc.getSeqMin();
+      viewer.setBgColour(panel.getRotatableCanvas().getBackgroundColour().getRGB());
+      viewer.setScaleFactor(panel.getRotatableCanvas().getScaleFactor());
+      float[] spMin = panel.getRotatableCanvas().getSeqMin();
       SeqPointMin spmin = new SeqPointMin();
       spmin.setXPos(spMin[0]);
       spmin.setYPos(spMin[1]);
       spmin.setZPos(spMin[2]);
       viewer.setSeqPointMin(spmin);
-      float[] spMax = panel.rc.getSeqMax();
+      float[] spMax = panel.getRotatableCanvas().getSeqMax();
       SeqPointMax spmax = new SeqPointMax();
       spmax.setXPos(spMax[0]);
       spmax.setYPos(spMax[1]);
       spmax.setZPos(spMax[2]);
       viewer.setSeqPointMax(spmax);
-      viewer.setShowLabels(panel.rc.showLabels);
-      viewer.setLinkToAllViews(panel.rc.applyToAllViews);
+      viewer.setShowLabels(panel.getRotatableCanvas().isShowLabels());
+      viewer.setLinkToAllViews(panel.getRotatableCanvas().isApplyToAllViews());
       SimilarityParamsI sp = pcaModel.getSimilarityParameters();
       viewer.setIncludeGaps(sp.includeGaps());
       viewer.setMatchGaps(sp.matchGaps());
@@ -1614,7 +1614,7 @@ public class Jalview2XML
       /*
        * (end points of) axes on display
        */
-      for (Point p : panel.rc.axisEndPoints)
+      for (Point p : panel.getRotatableCanvas().getAxisEndPoints())
       {
         Axis axis = new Axis();
         axis.setXPos(p.x);
@@ -5984,9 +5984,9 @@ public class Jalview2XML
   
         boolean showLabels = viewer.isShowLabels();
         panel.setShowLabels(showLabels);
-        panel.rc.showLabels = showLabels;
-        panel.rc.bgColour = new Color(viewer.getBgColour());
-        panel.rc.applyToAllViews = viewer.isLinkToAllViews();
+        panel.getRotatableCanvas().setShowLabels(showLabels);
+        panel.getRotatableCanvas().setBgColour(new Color(viewer.getBgColour()));
+        panel.getRotatableCanvas().setApplyToAllViews(viewer.isLinkToAllViews());
 
         /*
          * load PCA output data
@@ -6005,7 +6005,7 @@ public class Jalview2XML
         MatrixI result = loadDoubleMatrix(pcaData.getEigenMatrix());
         pca.setEigenmatrix(result);
 
-        panel.pcaModel.setPCA(pca);
+        panel.getPcaModel().setPCA(pca);
 
         /*
          * we haven't saved the input data! (JAL-2647 to do)
@@ -6030,30 +6030,30 @@ public class Jalview2XML
                   seq, pt);
           seqPoints.add(seqPoint);
         }
-        panel.rc.setPoints(seqPoints, seqPoints.size());
+        panel.getRotatableCanvas().setPoints(seqPoints, seqPoints.size());
 
         /*
          * set min-max ranges and scale after setPoints (which recomputes them)
          */
-        panel.rc.scaleFactor = viewer.getScaleFactor();
+        panel.getRotatableCanvas().setScaleFactor(viewer.getScaleFactor());
         SeqPointMin spMin = viewer.getSeqPointMin();
         float[] min = new float[] { spMin.getXPos(), spMin.getYPos(),
             spMin.getZPos() };
         SeqPointMax spMax = viewer.getSeqPointMax();
         float[] max = new float[] { spMax.getXPos(), spMax.getYPos(),
             spMax.getZPos() };
-        panel.rc.setSeqMinMax(min, max);
+        panel.getRotatableCanvas().setSeqMinMax(min, max);
 
         // todo: hold points list in PCAModel only
-        panel.pcaModel.setSequencePoints(seqPoints);
+        panel.getPcaModel().setSequencePoints(seqPoints);
 
         panel.setSelectedDimensionIndex(viewer.getXDim(), X);
         panel.setSelectedDimensionIndex(viewer.getYDim(), Y);
         panel.setSelectedDimensionIndex(viewer.getZDim(), Z);
 
         // is this duplication needed?
-        panel.top = seqPoints.size() - 1;
-        panel.pcaModel.setTop(seqPoints.size() - 1);
+        panel.setTop(seqPoints.size() - 1);
+        panel.getPcaModel().setTop(seqPoints.size() - 1);
 
         /*
          * add the axes' end points for the display
@@ -6061,7 +6061,7 @@ public class Jalview2XML
         for (int i = 0; i < 3; i++)
         {
           Axis axis = viewer.getAxis(i);
-          panel.rc.axisEndPoints[i] = new Point(axis.getXPos(),
+          panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point(axis.getXPos(),
                   axis.getYPos(), axis.getZPos());
         }
 
diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index da1dffe..df0cd03 100644
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.AlignViewportI;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
 import jalview.bin.Cache;
@@ -64,15 +65,15 @@ public class PCAPanel extends GPCAPanel
 
   private static final int MIN_HEIGHT = 250;
 
-  RotatableCanvas rc;
+  private RotatableCanvas rc;
 
   AlignmentPanel ap;
 
   AlignmentViewport av;
 
-  PCAModel pcaModel;
+  private PCAModel pcaModel;
 
-  int top = 0;
+  private int top = 0;
 
   private IProgressIndicator progressBar;
 
@@ -120,14 +121,14 @@ public class PCAPanel extends GPCAPanel
 
     ScoreModelI scoreModel = ScoreModels.getInstance()
             .getScoreModel(modelName, ap);
-    pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
-            params);
+    setPcaModel(new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
+            params));
     PaintRefresher.Register(this, av.getSequenceSetId());
 
-    rc = new RotatableCanvas(alignPanel);
-    this.getContentPane().add(rc, BorderLayout.CENTER);
+    setRotatableCanvas(new RotatableCanvas(alignPanel));
+    this.getContentPane().add(getRotatableCanvas(), BorderLayout.CENTER);
 
-    addKeyListener(rc);
+    addKeyListener(getRotatableCanvas());
     validate();
 
     this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
@@ -139,7 +140,7 @@ public class PCAPanel extends GPCAPanel
    */
   protected void close_actionPerformed()
   {
-    pcaModel = null;
+    setPcaModel(null);
   }
 
   @Override
@@ -147,13 +148,13 @@ public class PCAPanel extends GPCAPanel
   {
     Color col = JColorChooser.showDialog(this,
             MessageManager.getString("label.select_background_colour"),
-            rc.bgColour);
+            getRotatableCanvas().getBgColour());
 
     if (col != null)
     {
-      rc.bgColour = col;
+      getRotatableCanvas().setBgColour(col);
     }
-    rc.repaint();
+    getRotatableCanvas().repaint();
   }
 
   /**
@@ -174,15 +175,15 @@ public class PCAPanel extends GPCAPanel
     progress.setProgressBar(message, progId);
     try
     {
-      pcaModel.calculate();
+      getPcaModel().calculate();
 
       xCombobox.setSelectedIndex(0);
       yCombobox.setSelectedIndex(1);
       zCombobox.setSelectedIndex(2);
 
-      pcaModel.updateRc(rc);
+      getPcaModel().updateRc(getRotatableCanvas());
       // rc.invalidate();
-      top = pcaModel.getTop();
+      setTop(getPcaModel().getTop());
 
     } catch (OutOfMemoryError er)
     {
@@ -199,7 +200,7 @@ public class PCAPanel extends GPCAPanel
     {
       Desktop.addInternalFrame(this,
               MessageManager.formatMessage("label.calc_title", "PCA",
-                      pcaModel.getScoreModelName()),
+                      getPcaModel().getScoreModelName()),
               475, 450);
     }
     working = false;
@@ -212,16 +213,16 @@ public class PCAPanel extends GPCAPanel
   @Override
   protected void doDimensionChange()
   {
-    if (top == 0)
+    if (getTop() == 0)
     {
       return;
     }
 
-    int dim1 = top - xCombobox.getSelectedIndex();
-    int dim2 = top - yCombobox.getSelectedIndex();
-    int dim3 = top - zCombobox.getSelectedIndex();
-    pcaModel.updateRcView(dim1, dim2, dim3);
-    rc.resetView();
+    int dim1 = getTop() - xCombobox.getSelectedIndex();
+    int dim2 = getTop() - yCombobox.getSelectedIndex();
+    int dim3 = getTop() - zCombobox.getSelectedIndex();
+    getPcaModel().updateRcView(dim1, dim2, dim3);
+    getRotatableCanvas().resetView();
   }
 
   /**
@@ -254,7 +255,7 @@ public class PCAPanel extends GPCAPanel
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     try
     {
-      cap.setText(pcaModel.getDetails());
+      cap.setText(getPcaModel().getDetails());
       Desktop.addInternalFrame(cap,
               MessageManager.getString("label.pca_details"), 500, 500);
     } catch (OutOfMemoryError oom)
@@ -267,7 +268,7 @@ public class PCAPanel extends GPCAPanel
   @Override
   protected void showLabels_actionPerformed()
   {
-    rc.showLabels(showLabels.getState());
+    getRotatableCanvas().showLabels(showLabels.getState());
   }
 
   @Override
@@ -285,7 +286,7 @@ public class PCAPanel extends GPCAPanel
   public void originalSeqData_actionPerformed()
   {
     // JAL-2647 disabled after load from project (until save to project done)
-    if (pcaModel.getInputData() == null)
+    if (getPcaModel().getInputData() == null)
     {
       Cache.log.info(
               "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
@@ -307,7 +308,7 @@ public class PCAPanel extends GPCAPanel
     {
     }
 
-    Object[] alAndColsel = pcaModel.getInputData()
+    Object[] alAndColsel = getPcaModel().getInputData()
             .getAlignmentAndHiddenColumns(gc);
 
     if (alAndColsel != null && alAndColsel[0] != null)
@@ -389,11 +390,11 @@ public class PCAPanel extends GPCAPanel
     {
       pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
 
-      rc.drawBackground(pg);
-      rc.drawScene(pg);
-      if (rc.drawAxes)
+      getRotatableCanvas().drawBackground(pg);
+      getRotatableCanvas().drawScene(pg);
+      if (getRotatableCanvas().drawAxes)
       {
-        rc.drawAxes(pg);
+        getRotatableCanvas().drawAxes(pg);
       }
 
       if (pi == 0)
@@ -427,8 +428,8 @@ public class PCAPanel extends GPCAPanel
 
   void makePCAImage(ImageMaker.TYPE type)
   {
-    int width = rc.getWidth();
-    int height = rc.getHeight();
+    int width = getRotatableCanvas().getWidth();
+    int height = getRotatableCanvas().getHeight();
 
     ImageMaker im;
 
@@ -452,11 +453,11 @@ public class PCAPanel extends GPCAPanel
 
     if (im.getGraphics() != null)
     {
-      rc.drawBackground(im.getGraphics());
-      rc.drawScene(im.getGraphics());
-      if (rc.drawAxes)
+      getRotatableCanvas().drawBackground(im.getGraphics());
+      getRotatableCanvas().drawScene(im.getGraphics());
+      if (getRotatableCanvas().drawAxes)
       {
-        rc.drawAxes(im.getGraphics());
+        getRotatableCanvas().drawAxes(im.getGraphics());
       }
       im.writeImage();
     }
@@ -476,7 +477,7 @@ public class PCAPanel extends GPCAPanel
   {
     AlignmentPanel[] aps = PaintRefresher
             .getAssociatedPanels(av.getSequenceSetId());
-    if (aps.length == 1 && rc.av == aps[0].av)
+    if (aps.length == 1 && getRotatableCanvas().av == aps[0].av)
     {
       associateViewsMenu.setVisible(false);
       return;
@@ -498,17 +499,18 @@ public class PCAPanel extends GPCAPanel
 
     for (int i = 0; i < iSize; i++)
     {
-      final AlignmentPanel ap = aps[i];
-      item = new JRadioButtonMenuItem(ap.av.getViewName(), ap.av == rc.av);
+      final AlignmentPanel panel = aps[i];
+      item = new JRadioButtonMenuItem(panel.av.getViewName(),
+              panel.av == getRotatableCanvas().av);
       buttonGroup.add(item);
       item.addActionListener(new ActionListener()
       {
         @Override
         public void actionPerformed(ActionEvent evt)
         {
-          rc.applyToAllViews = false;
-          rc.av = panel.av;
-          rc.ap = panel;
+          getRotatableCanvas().setApplyToAllViews(false);
+          getRotatableCanvas().av = panel.av;
+          getRotatableCanvas().ap = panel;
           PaintRefresher.Register(PCAPanel.this,
                   panel.av.getSequenceSetId());
         }
@@ -522,13 +524,13 @@ public class PCAPanel extends GPCAPanel
 
     buttonGroup.add(itemf);
 
-    itemf.setSelected(rc.applyToAllViews);
+    itemf.setSelected(getRotatableCanvas().isApplyToAllViews());
     itemf.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent evt)
       {
-        rc.applyToAllViews = itemf.isSelected();
+        getRotatableCanvas().setApplyToAllViews(itemf.isSelected());
       }
     });
     associateViewsMenu.add(itemf);
@@ -548,7 +550,7 @@ public class PCAPanel extends GPCAPanel
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     try
     {
-      cap.setText(pcaModel.getPointsasCsv(false,
+      cap.setText(getPcaModel().getPointsasCsv(false,
               xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
               zCombobox.getSelectedIndex()));
       Desktop.addInternalFrame(cap, MessageManager
@@ -574,7 +576,7 @@ public class PCAPanel extends GPCAPanel
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     try
     {
-      cap.setText(pcaModel.getPointsasCsv(true,
+      cap.setText(getPcaModel().getPointsasCsv(true,
               xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
               zCombobox.getSelectedIndex()));
       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
@@ -686,11 +688,11 @@ public class PCAPanel extends GPCAPanel
   @Override
   protected void resetButton_actionPerformed()
   {
-    int t = top;
-    top = 0; // ugly - prevents dimensionChanged events from being processed
+    int t = getTop();
+    setTop(0); // ugly - prevents dimensionChanged events from being processed
     xCombobox.setSelectedIndex(0);
     yCombobox.setSelectedIndex(1);
-    top = t;
+    setTop(t);
     zCombobox.setSelectedIndex(2);
   }
 
@@ -738,7 +740,42 @@ public class PCAPanel extends GPCAPanel
    */
   public void setInputData(AlignmentView data)
   {
-    pcaModel.setInputData(data);
+    getPcaModel().setInputData(data);
     originalSeqData.setVisible(data != null);
   }
+
+  public AlignViewportI getAlignViewport()
+  {
+    return av;
+  }
+
+  public PCAModel getPcaModel()
+  {
+    return pcaModel;
+  }
+
+  public void setPcaModel(PCAModel pcaModel)
+  {
+    this.pcaModel = pcaModel;
+  }
+
+  public RotatableCanvas getRotatableCanvas()
+  {
+    return rc;
+  }
+
+  public void setRotatableCanvas(RotatableCanvas rc)
+  {
+    this.rc = rc;
+  }
+
+  public int getTop()
+  {
+    return top;
+  }
+
+  public void setTop(int top)
+  {
+    this.top = top;
+  }
 }
diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index b00055b..dc0cdb4 100755
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -104,7 +104,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
    * half the available width or height (whichever is less); increase this
    * factor to zoom in, decrease it to zoom out
    */
-  float scaleFactor;
+  private float scaleFactor;
 
   int npoint;
 
@@ -116,7 +116,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
   /*
    * x, y, z axis end points (PCA dimension values)
    */
-  Point[] axisEndPoints;
+  private Point[] axisEndPoints;
 
   // fields for 'select rectangle' (JAL-1124)
   // int rectx1;
@@ -128,11 +128,11 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 
   AlignmentPanel ap;
 
-  boolean showLabels;
+  private boolean showLabels;
 
-  Color bgColour;
+  private Color bgColour;
 
-  boolean applyToAllViews;
+  private boolean applyToAllViews;
 
   /**
    * Constructor
@@ -143,10 +143,10 @@ public class RotatableCanvas extends JPanel implements MouseListener,
   {
     this.av = panel.av;
     this.ap = panel;
-    axisEndPoints = new Point[DIMS];
-    showLabels = false;
-    applyToAllViews = false;
-    bgColour = Color.BLACK;
+    setAxisEndPoints(new Point[DIMS]);
+    setShowLabels(false);
+    setApplyToAllViews(false);
+    setBgColour(Color.BLACK);
     resetAxes();
 
     ToolTipManager.sharedInstance().registerComponent(this);
@@ -163,7 +163,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
    */
   public void showLabels(boolean show)
   {
-    showLabels = show;
+    setShowLabels(show);
     repaint();
   }
 
@@ -176,7 +176,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 
     findWidths();
 
-    scaleFactor = 1f;
+    setScaleFactor(1f);
   }
 
   /**
@@ -185,9 +185,9 @@ public class RotatableCanvas extends JPanel implements MouseListener,
    */
   protected void resetAxes()
   {
-    axisEndPoints[0] = new Point(1f, 0f, 0f);
-    axisEndPoints[1] = new Point(0f, 1f, 0f);
-    axisEndPoints[2] = new Point(0f, 0f, 1f);
+    getAxisEndPoints()[0] = new Point(1f, 0f, 0f);
+    getAxisEndPoints()[1] = new Point(0f, 1f, 0f);
+    getAxisEndPoints()[2] = new Point(0f, 0f, 1f);
   }
 
   /**
@@ -325,13 +325,13 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     float maxWidth = Math.max(Math.abs(seqMax[0] - seqMin[0]),
             Math.abs(seqMax[1] - seqMin[1]));
     int pix = Math.min(getWidth(), getHeight());
-    float scaleBy = pix * scaleFactor / (2f * maxWidth);
+    float scaleBy = pix * getScaleFactor() / (2f * maxWidth);
 
     for (int i = 0; i < DIMS; i++)
     {
       g.drawLine(midX, midY,
-              midX + (int) (axisEndPoints[i].x * scaleBy * seqMax[0]),
-              midY + (int) (axisEndPoints[i].y * scaleBy * seqMax[1]));
+              midX + (int) (getAxisEndPoints()[i].x * scaleBy * seqMax[0]),
+              midY + (int) (getAxisEndPoints()[i].y * scaleBy * seqMax[1]));
     }
   }
 
@@ -342,7 +342,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
    */
   public void drawBackground(Graphics g)
   {
-    g.setColor(bgColour);
+    g.setColor(getBgColour());
     g.fillRect(0, 0, prefSize.width, prefSize.height);
   }
 
@@ -365,7 +365,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     float xWidth = Math.abs(seqMax[0] - seqMin[0]);
     float yWidth = Math.abs(seqMax[1] - seqMin[1]);
     float maxWidth = Math.max(xWidth, yWidth);
-    float scaleBy = pix * scaleFactor / (2f * maxWidth);
+    float scaleBy = pix * getScaleFactor() / (2f * maxWidth);
 
     float[] centre = getCentre();
 
@@ -385,19 +385,19 @@ public class RotatableCanvas extends JPanel implements MouseListener,
       int y = (int) ((sp.coord.y - centre[1]) * scaleBy) + halfheight;
       g.fillRect(x - 3, y - 3, 6, 6);
 
-      if (showLabels)
+      if (isShowLabels())
       {
         g.setColor(Color.red);
         g.drawString(sp.getSequence().getName(), x - 3, y - 4);
       }
     }
-    if (showLabels)
+    if (isShowLabels())
     {
       g.setColor(AXIS_COLOUR);
       int midX = getWidth() / 2;
       int midY = getHeight() / 2;
       Iterator<String> axes = AXES.iterator();
-      for (Point p : axisEndPoints)
+      for (Point p : getAxisEndPoints())
       {
         int x = midX + (int) (p.x * scaleBy * seqMax[0]);
         int y = midY + (int) (p.y * scaleBy * seqMax[1]);
@@ -525,7 +525,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
   {
     if (factor > 0f)
     {
-      scaleFactor *= factor;
+      setScaleFactor(getScaleFactor() * factor);
     }
   }
 
@@ -712,7 +712,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
      */
     for (int i = 0; i < DIMS; i++)
     {
-      axisEndPoints[i] = rotmat.vectorMultiply(axisEndPoints[i]);
+      getAxisEndPoints()[i] = rotmat.vectorMultiply(getAxisEndPoints()[i]);
     }
   }
 
@@ -748,9 +748,9 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     for (int i = 0; i < npoint; i++)
     {
       SequencePoint sp = sequencePoints.get(i);
-      int tmp1 = (int) (((sp.coord.x - centre[0]) * scaleFactor)
+      int tmp1 = (int) (((sp.coord.x - centre[0]) * getScaleFactor())
               + (getWidth() / 2.0));
-      int tmp2 = (int) (((sp.coord.y - centre[1]) * scaleFactor)
+      int tmp2 = (int) (((sp.coord.y - centre[1]) * getScaleFactor())
               + (getHeight() / 2.0));
 
       if ((tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2))
@@ -787,7 +787,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     float xWidth = Math.abs(seqMax[0] - seqMin[0]);
     float yWidth = Math.abs(seqMax[1] - seqMin[1]);
     float maxWidth = Math.max(xWidth, yWidth);
-    float scaleBy = pix * scaleFactor / (2f * maxWidth);
+    float scaleBy = pix * getScaleFactor() / (2f * maxWidth);
 
     float[] centre = getCentre();
 
@@ -824,7 +824,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
    */
   AlignmentPanel[] getAssociatedPanels()
   {
-    if (applyToAllViews)
+    if (isApplyToAllViews())
     {
       return PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
     }
@@ -836,7 +836,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 
   public Color getBackgroundColour()
   {
-    return bgColour;
+    return getBgColour();
   }
 
   /**
@@ -894,4 +894,54 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     seqMin = min;
     seqMax = max;
   }
+
+  public float getScaleFactor()
+  {
+    return scaleFactor;
+  }
+
+  public void setScaleFactor(float scaleFactor)
+  {
+    this.scaleFactor = scaleFactor;
+  }
+
+  public boolean isShowLabels()
+  {
+    return showLabels;
+  }
+
+  public void setShowLabels(boolean showLabels)
+  {
+    this.showLabels = showLabels;
+  }
+
+  public boolean isApplyToAllViews()
+  {
+    return applyToAllViews;
+  }
+
+  public void setApplyToAllViews(boolean applyToAllViews)
+  {
+    this.applyToAllViews = applyToAllViews;
+  }
+
+  public Point[] getAxisEndPoints()
+  {
+    return axisEndPoints;
+  }
+
+  public void setAxisEndPoints(Point[] axisEndPoints)
+  {
+    this.axisEndPoints = axisEndPoints;
+  }
+
+  public Color getBgColour()
+  {
+    return bgColour;
+  }
+
+  public void setBgColour(Color bgColour)
+  {
+    this.bgColour = bgColour;
+  }
 }
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 45def89..c195c80 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -1160,4 +1160,14 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   {
     this.threshold = threshold;
   }
+
+  public boolean isApplyToAllViews()
+  {
+    return this.applyToAllViews;
+  }
+
+  public void setApplyToAllViews(boolean applyToAllViews)
+  {
+    this.applyToAllViews = applyToAllViews;
+  }
 }
diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 90c09d7..9f796f2 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -20,9 +20,18 @@
  */
 package jalview.project;
 
+import static jalview.math.RotatableMatrix.Axis.X;
+import static jalview.math.RotatableMatrix.Axis.Y;
+import static jalview.math.RotatableMatrix.Axis.Z;
+
 import jalview.analysis.Conservation;
+import jalview.analysis.PCA;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.analysis.scoremodels.SimilarityParams;
 import jalview.api.FeatureColourI;
 import jalview.api.ViewStyleI;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignedCodonFrame;
@@ -31,6 +40,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Point;
 import jalview.datamodel.RnaViewerModel;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
@@ -52,6 +62,7 @@ import jalview.gui.FeatureRenderer;
 import jalview.gui.Jalview2XML_V1;
 import jalview.gui.JvOptionPane;
 import jalview.gui.OOMWarning;
+import jalview.gui.PCAPanel;
 import jalview.gui.PaintRefresher;
 import jalview.gui.SplitFrame;
 import jalview.gui.StructureViewer;
@@ -61,6 +72,8 @@ import jalview.gui.TreePanel;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.NewickFile;
+import jalview.math.Matrix;
+import jalview.math.MatrixI;
 import jalview.renderer.ResidueShaderI;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.ColourSchemeI;
@@ -77,6 +90,7 @@ import jalview.util.StringUtils;
 import jalview.util.jarInputStreamProvider;
 import jalview.util.matcher.Condition;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.PCAModel;
 import jalview.viewmodel.ViewportRanges;
 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
@@ -92,6 +106,8 @@ import jalview.xml.binding.jalview.Annotation;
 import jalview.xml.binding.jalview.Annotation.ThresholdLine;
 import jalview.xml.binding.jalview.AnnotationColourScheme;
 import jalview.xml.binding.jalview.AnnotationElement;
+import jalview.xml.binding.jalview.DoubleMatrix;
+import jalview.xml.binding.jalview.DoubleVector;
 import jalview.xml.binding.jalview.Feature;
 import jalview.xml.binding.jalview.Feature.OtherData;
 import jalview.xml.binding.jalview.FeatureMatcherSet.CompoundMatcher;
@@ -106,6 +122,11 @@ import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids;
 import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.StructureState;
 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer;
 import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer.SecondaryStructure;
+import jalview.xml.binding.jalview.JalviewModel.PcaViewer;
+import jalview.xml.binding.jalview.JalviewModel.PcaViewer.Axis;
+import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMax;
+import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMin;
+import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SequencePoint;
 import jalview.xml.binding.jalview.JalviewModel.Tree;
 import jalview.xml.binding.jalview.JalviewModel.UserColours;
 import jalview.xml.binding.jalview.JalviewModel.Viewport;
@@ -118,6 +139,7 @@ import jalview.xml.binding.jalview.MapListType.MapListTo;
 import jalview.xml.binding.jalview.Mapping;
 import jalview.xml.binding.jalview.NoValueColour;
 import jalview.xml.binding.jalview.ObjectFactory;
+import jalview.xml.binding.jalview.PcaDataType;
 import jalview.xml.binding.jalview.Pdbentry.Property;
 import jalview.xml.binding.jalview.Sequence;
 import jalview.xml.binding.jalview.Sequence.DBRef;
@@ -1215,6 +1237,9 @@ public class Jalview2XML
               tree.setXpos(tp.getX());
               tree.setYpos(tp.getY());
               tree.setId(makeHashCode(tp, null));
+              tree.setLinkToAllViews(
+                      tp.getTreeCanvas().isApplyToAllViews());
+
               // jms.addTree(tree);
               object.getTree().add(tree);
             }
@@ -1223,6 +1248,24 @@ public class Jalview2XML
       }
     }
 
+    /*
+     * save PCA viewers
+     */
+    if (!storeDS && Desktop.desktop != null)
+    {
+      for (JInternalFrame frame : Desktop.desktop.getAllFrames())
+      {
+        if (frame instanceof PCAPanel)
+        {
+          PCAPanel panel = (PCAPanel) frame;
+          if (panel.getAlignViewport().getAlignment() == jal)
+          {
+            savePCA(panel, object);
+          }
+        }
+      }
+    }
+
     // SAVE ANNOTATIONS
     /**
      * store forward refs from an annotationRow to any groups
@@ -1630,6 +1673,198 @@ public class Jalview2XML
   }
 
   /**
+   * Writes PCA viewer attributes and computed values to an XML model object and
+   * adds it to the JalviewModel. Any exceptions are reported by logging.
+   */
+  protected void savePCA(PCAPanel panel, JalviewModel object)
+  {
+    try
+    {
+      PcaViewer viewer = new PcaViewer();
+      viewer.setHeight(panel.getHeight());
+      viewer.setWidth(panel.getWidth());
+      viewer.setXpos(panel.getX());
+      viewer.setYpos(panel.getY());
+      viewer.setTitle(panel.getTitle());
+      PCAModel pcaModel = panel.getPcaModel();
+      viewer.setScoreModelName(pcaModel.getScoreModelName());
+      viewer.setXDim(panel.getSelectedDimensionIndex(X));
+      viewer.setYDim(panel.getSelectedDimensionIndex(Y));
+      viewer.setZDim(panel.getSelectedDimensionIndex(Z));
+      viewer.setBgColour(
+              panel.getRotatableCanvas().getBackgroundColour().getRGB());
+      viewer.setScaleFactor(panel.getRotatableCanvas().getScaleFactor());
+      float[] spMin = panel.getRotatableCanvas().getSeqMin();
+      SeqPointMin spmin = new SeqPointMin();
+      spmin.setXPos(spMin[0]);
+      spmin.setYPos(spMin[1]);
+      spmin.setZPos(spMin[2]);
+      viewer.setSeqPointMin(spmin);
+      float[] spMax = panel.getRotatableCanvas().getSeqMax();
+      SeqPointMax spmax = new SeqPointMax();
+      spmax.setXPos(spMax[0]);
+      spmax.setYPos(spMax[1]);
+      spmax.setZPos(spMax[2]);
+      viewer.setSeqPointMax(spmax);
+      viewer.setShowLabels(panel.getRotatableCanvas().isShowLabels());
+      viewer.setLinkToAllViews(
+              panel.getRotatableCanvas().isApplyToAllViews());
+      SimilarityParamsI sp = pcaModel.getSimilarityParameters();
+      viewer.setIncludeGaps(sp.includeGaps());
+      viewer.setMatchGaps(sp.matchGaps());
+      viewer.setIncludeGappedColumns(sp.includeGappedColumns());
+      viewer.setDenominateByShortestLength(sp.denominateByShortestLength());
+
+      /*
+       * sequence points on display
+       */
+      for (jalview.datamodel.SequencePoint spt : pcaModel
+              .getSequencePoints())
+      {
+        SequencePoint point = new SequencePoint();
+        point.setSequenceRef(seqHash(spt.getSequence()));
+        point.setXPos(spt.coord.x);
+        point.setYPos(spt.coord.y);
+        point.setZPos(spt.coord.z);
+        viewer.getSequencePoint().add(point);
+      }
+
+      /*
+       * (end points of) axes on display
+       */
+      for (Point p : panel.getRotatableCanvas().getAxisEndPoints())
+      {
+
+        Axis axis = new Axis();
+        axis.setXPos(p.x);
+        axis.setYPos(p.y);
+        axis.setZPos(p.z);
+        viewer.getAxis().add(axis);
+      }
+
+      /*
+       * raw PCA data (note we are not restoring PCA inputs here -
+       * alignment view, score model, similarity parameters)
+       */
+      PcaDataType data = new PcaDataType();
+      viewer.setPcaData(data);
+      PCA pca = pcaModel.getPcaData();
+
+      DoubleMatrix pm = new DoubleMatrix();
+      saveDoubleMatrix(pca.getPairwiseScores(), pm);
+      data.setPairwiseMatrix(pm);
+
+      DoubleMatrix tm = new DoubleMatrix();
+      saveDoubleMatrix(pca.getTridiagonal(), tm);
+      data.setTridiagonalMatrix(tm);
+
+      DoubleMatrix eigenMatrix = new DoubleMatrix();
+      data.setEigenMatrix(eigenMatrix);
+      saveDoubleMatrix(pca.getEigenmatrix(), eigenMatrix);
+
+      object.getPcaViewer().add(viewer);
+    } catch (Throwable t)
+    {
+      Cache.log.error("Error saving PCA: " + t.getMessage());
+    }
+  }
+
+  /**
+   * Stores values from a matrix into an XML element, including (if present) the
+   * D or E vectors
+   * 
+   * @param m
+   * @param xmlMatrix
+   * @see #loadDoubleMatrix(DoubleMatrix)
+   */
+  protected void saveDoubleMatrix(MatrixI m, DoubleMatrix xmlMatrix)
+  {
+    xmlMatrix.setRows(m.height());
+    xmlMatrix.setColumns(m.width());
+    for (int i = 0; i < m.height(); i++)
+    {
+      DoubleVector row = new DoubleVector();
+      for (int j = 0; j < m.width(); j++)
+      {
+        row.getV().add(m.getValue(i, j));
+      }
+      xmlMatrix.getRow().add(row);
+    }
+    if (m.getD() != null)
+    {
+      DoubleVector dVector = new DoubleVector();
+      for (double d : m.getD())
+      {
+        dVector.getV().add(d);
+      }
+      xmlMatrix.setD(dVector);
+    }
+    if (m.getE() != null)
+    {
+      DoubleVector eVector = new DoubleVector();
+      for (double e : m.getE())
+      {
+        eVector.getV().add(e);
+      }
+      xmlMatrix.setE(eVector);
+    }
+  }
+
+  /**
+   * Loads XML matrix data into a new Matrix object, including the D and/or E
+   * vectors (if present)
+   * 
+   * @param mData
+   * @return
+   * @see Jalview2XML#saveDoubleMatrix(MatrixI, DoubleMatrix)
+   */
+  protected MatrixI loadDoubleMatrix(DoubleMatrix mData)
+  {
+    int rows = mData.getRows();
+    double[][] vals = new double[rows][];
+    List<Double> dVector;
+    double[] vec;
+
+    for (int i = 0; i < rows; i++)
+    {
+      dVector = mData.getRow().get(i).getV();
+      vals[i] = new double[dVector.size()];
+      int dvi = 0;
+      for (Double d : dVector)
+      {
+        vals[i][dvi++] = d;
+      }
+    }
+
+    MatrixI m = new Matrix(vals);
+
+    if (mData.getD() != null)
+    {
+      dVector = mData.getD().getV();
+      vec = new double[dVector.size()];
+      int dvi = 0;
+      for (Double d : dVector)
+      {
+        vec[dvi++] = d;
+      }
+      m.setD(vec);
+    }
+    if (mData.getE() != null)
+    {
+      dVector = mData.getE().getV();
+      vec = new double[dVector.size()];
+      int dvi = 0;
+      for (Double d : dVector)
+      {
+        vec[dvi++] = d;
+      }
+      m.setE(vec);
+    }
+
+    return m;
+  }
+
+  /**
    * Save any Varna viewers linked to this sequence. Writes an rnaViewer element
    * for each viewer, with
    * <ul>
@@ -3799,6 +4034,7 @@ public class Jalview2XML
     if (loadTreesAndStructures)
     {
       loadTrees(jalviewModel, view, af, av, ap);
+      loadPCAViewers(jalviewModel, ap);
       loadPDBStructures(jprovider, jseqs, af, ap);
       loadRnaViewers(jprovider, jseqs, ap);
     }
@@ -3947,6 +4183,8 @@ public class Jalview2XML
           // TODO: verify 'associate with all views' works still
           tp.getTreeCanvas().setViewport(av); // af.viewport;
           tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
+          // FIXME: should we use safeBoolean here ?
+          tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
 
         }
         if (tp == null)
@@ -5935,6 +6173,128 @@ public class Jalview2XML
   }
 
   /**
+   * Loads any saved PCA viewers
+   * 
+   * @param jms
+   * @param ap
+   */
+  protected void loadPCAViewers(JalviewModel model, AlignmentPanel ap)
+  {
+    try
+    {
+      List<PcaViewer> pcaviewers = model.getPcaViewer();
+      for (PcaViewer viewer : pcaviewers)
+      {
+        String modelName = viewer.getScoreModelName();
+        SimilarityParamsI params = new SimilarityParams(
+                viewer.isIncludeGappedColumns(), viewer.isMatchGaps(),
+                viewer.isIncludeGaps(),
+                viewer.isDenominateByShortestLength());
+
+        /*
+         * create the panel (without computing the PCA)
+         */
+        PCAPanel panel = new PCAPanel(ap, modelName, params);
+
+        panel.setTitle(viewer.getTitle());
+        panel.setBounds(new Rectangle(viewer.getXpos(), viewer.getYpos(),
+                viewer.getWidth(), viewer.getHeight()));
+
+        boolean showLabels = viewer.isShowLabels();
+        panel.setShowLabels(showLabels);
+        panel.getRotatableCanvas().setShowLabels(showLabels);
+        panel.getRotatableCanvas()
+                .setBgColour(new Color(viewer.getBgColour()));
+        panel.getRotatableCanvas()
+                .setApplyToAllViews(viewer.isLinkToAllViews());
+
+        /*
+         * load PCA output data
+         */
+        ScoreModelI scoreModel = ScoreModels.getInstance()
+                .getScoreModel(modelName, ap);
+        PCA pca = new PCA(null, scoreModel, params);
+        PcaDataType pcaData = viewer.getPcaData();
+
+        MatrixI pairwise = loadDoubleMatrix(pcaData.getPairwiseMatrix());
+        pca.setPairwiseScores(pairwise);
+
+        MatrixI triDiag = loadDoubleMatrix(pcaData.getTridiagonalMatrix());
+        pca.setTridiagonal(triDiag);
+
+        MatrixI result = loadDoubleMatrix(pcaData.getEigenMatrix());
+        pca.setEigenmatrix(result);
+
+        panel.getPcaModel().setPCA(pca);
+
+        /*
+         * we haven't saved the input data! (JAL-2647 to do)
+         */
+        panel.setInputData(null);
+
+        /*
+         * add the sequence points for the PCA display
+         */
+        List<jalview.datamodel.SequencePoint> seqPoints = new ArrayList<>();
+        for (SequencePoint sp : viewer.getSequencePoint())
+        {
+          String seqId = sp.getSequenceRef();
+          SequenceI seq = seqRefIds.get(seqId);
+          if (seq == null)
+          {
+            throw new IllegalStateException(
+                    "Unmatched seqref for PCA: " + seqId);
+          }
+          Point pt = new Point(sp.getXPos(), sp.getYPos(), sp.getZPos());
+          jalview.datamodel.SequencePoint seqPoint = new jalview.datamodel.SequencePoint(
+                  seq, pt);
+          seqPoints.add(seqPoint);
+        }
+        panel.getRotatableCanvas().setPoints(seqPoints, seqPoints.size());
+
+        /*
+         * set min-max ranges and scale after setPoints (which recomputes them)
+         */
+        panel.getRotatableCanvas().setScaleFactor(viewer.getScaleFactor());
+        SeqPointMin spMin = viewer.getSeqPointMin();
+        float[] min = new float[] { spMin.getXPos(), spMin.getYPos(),
+            spMin.getZPos() };
+        SeqPointMax spMax = viewer.getSeqPointMax();
+        float[] max = new float[] { spMax.getXPos(), spMax.getYPos(),
+            spMax.getZPos() };
+        panel.getRotatableCanvas().setSeqMinMax(min, max);
+
+        // todo: hold points list in PCAModel only
+        panel.getPcaModel().setSequencePoints(seqPoints);
+
+        panel.setSelectedDimensionIndex(viewer.getXDim(), X);
+        panel.setSelectedDimensionIndex(viewer.getYDim(), Y);
+        panel.setSelectedDimensionIndex(viewer.getZDim(), Z);
+
+        // is this duplication needed?
+        panel.setTop(seqPoints.size() - 1);
+        panel.getPcaModel().setTop(seqPoints.size() - 1);
+
+        /*
+         * add the axes' end points for the display
+         */
+        for (int i = 0; i < 3; i++)
+        {
+          Axis axis = viewer.getAxis().get(i);
+          panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point(
+                  axis.getXPos(), axis.getYPos(), axis.getZPos());
+        }
+
+        Desktop.addInternalFrame(panel, MessageManager.formatMessage(
+                "label.calc_title", "PCA", modelName), 475, 450);
+      }
+    } catch (Exception ex)
+    {
+      Cache.log.error("Error loading PCA: " + ex.toString());
+    }
+  }
+
+  /**
    * Populates an XML model of the feature colour scheme for one feature type
    * 
    * @param featureType
diff --git a/src/jalview/xml/binding/jalview/AlcodonFrame.java b/src/jalview/xml/binding/jalview/AlcodonFrame.java
index 370ecc5..83f1ee2 100644
--- a/src/jalview/xml/binding/jalview/AlcodonFrame.java
+++ b/src/jalview/xml/binding/jalview/AlcodonFrame.java
@@ -2,7 +2,7 @@
 // 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: 2018.09.28 at 12:18:54 PM BST 
+// Generated on: 2018.12.20 at 11:47:26 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/Annotation.java b/src/jalview/xml/binding/jalview/Annotation.java
index 148406e..0dbcad0 100644
--- a/src/jalview/xml/binding/jalview/Annotation.java
+++ b/src/jalview/xml/binding/jalview/Annotation.java
@@ -2,7 +2,7 @@
 // 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: 2018.09.28 at 12:18:54 PM BST 
+// Generated on: 2018.12.20 at 11:47:26 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
index c9ee5f1..44affa2 100644
--- a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
+++ b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
@@ -2,7 +2,7 @@
 // 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: 2018.09.28 at 12:18:54 PM BST 
+// Generated on: 2018.12.20 at 11:47:26 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/AnnotationElement.java b/src/jalview/xml/binding/jalview/AnnotationElement.java
index 8cbd4fe..de408d2 100644
--- a/src/jalview/xml/binding/jalview/AnnotationElement.java
+++ b/src/jalview/xml/binding/jalview/AnnotationElement.java
@@ -2,7 +2,7 @@
 // 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: 2018.09.28 at 12:18:54 PM BST 
+// Generated on: 2018.12.20 at 11:47:26 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/DoubleMatrix.java b/src/jalview/xml/binding/jalview/DoubleMatrix.java
new file mode 100644
index 0000000..b4c07bc
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/DoubleMatrix.java
@@ -0,0 +1,186 @@
+//
+// 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: 2018.12.20 at 11:47:26 AM GMT 
+//
+
+
+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.XmlType;
+
+
+/**
+ * <p>Java class for DoubleMatrix complex type.
+ * 
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * 
+ * <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.
+     * 
+     * <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;
+    }
+
+}
diff --git a/src/jalview/xml/binding/jalview/DoubleVector.java b/src/jalview/xml/binding/jalview/DoubleVector.java
new file mode 100644
index 0000000..e2592ab
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/DoubleVector.java
@@ -0,0 +1,76 @@
+//
+// 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: 2018.12.20 at 11:47:26 AM GMT 
+//
+
+
+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.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for DoubleVector complex type.
+ * 
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * 
+ * <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 {
+
+    @XmlElement(type = Double.class)
+    protected List<Double> v;
+
+    /**
+     * 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;
+    }
+
+}
diff --git a/src/jalview/xml/binding/jalview/Feature.java b/src/jalview/xml/binding/jalview/Feature.java
index 7585f83..9001ee2 100644
--- a/src/jalview/xml/binding/jalview/Feature.java
+++ b/src/jalview/xml/binding/jalview/Feature.java
@@ -2,7 +2,7 @@
 // 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: 2018.09.28 at 12:18:54 PM BST 
+// Generated on: 2018.12.20 at 11:47:26 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/FeatureMatcher.java b/src/jalview/xml/binding/jalview/FeatureMatcher.java
index 3161408..0daf56a 100644
--- a/src/jalview/xml/binding/jalview/FeatureMatcher.java
+++ b/src/jalview/xml/binding/jalview/FeatureMatcher.java
@@ -2,7 +2,7 @@
 // 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: 2018.09.28 at 12:18:54 PM BST 
+// Generated on: 2018.12.20 at 11:47:26 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
index 5e181a1..bf69d5b 100644
--- a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
+++ b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
@@ -2,7 +2,7 @@
 // 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: 2018.09.28 at 12:18:54 PM BST 
+// Generated on: 2018.12.20 at 11:47:26 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/FilterBy.java b/src/jalview/xml/binding/jalview/FilterBy.java
index a854b63..5684acf 100644
--- a/src/jalview/xml/binding/jalview/FilterBy.java
+++ b/src/jalview/xml/binding/jalview/FilterBy.java
@@ -2,7 +2,7 @@
 // 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: 2018.09.28 at 12:18:54 PM BST 
+// Generated on: 2018.12.20 at 11:47:26 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/JalviewModel.java b/src/jalview/xml/binding/jalview/JalviewModel.java
index 0f538f2..ed57edc 100644
--- a/src/jalview/xml/binding/jalview/JalviewModel.java
+++ b/src/jalview/xml/binding/jalview/JalviewModel.java
@@ -2,7 +2,7 @@
 // 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: 2018.09.28 at 12:18:54 PM BST 
+// Generated on: 2018.12.20 at 11:47:26 AM GMT 
 //
 
 
@@ -243,6 +243,66 @@ import javax.xml.datatype.XMLGregorianCalendar;
  *                   &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}swingwindow"/>
+ *                   &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
+ *                   &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>
@@ -310,6 +370,7 @@ import javax.xml.datatype.XMLGregorianCalendar;
     "viewport",
     "userColours",
     "tree",
+    "pcaViewer",
     "featureSettings"
 })
 public class JalviewModel {
@@ -330,6 +391,8 @@ public class JalviewModel {
     @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;
 
@@ -551,6 +614,35 @@ public class JalviewModel {
     }
 
     /**
+     * Gets the value of the pcaViewer 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 pcaViewer property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getPcaViewer().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * 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
@@ -2974,21 +3066,57 @@ public class JalviewModel {
      * &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;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}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;attGroup ref="{www.jalview.org}SimilarityParams"/>
+     *       &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>
@@ -2998,38 +3126,42 @@ public class JalviewModel {
      */
     @XmlAccessorType(XmlAccessType.FIELD)
     @XmlType(name = "", propOrder = {
-        "title",
-        "newick"
+        "sequencePoint",
+        "axis",
+        "seqPointMin",
+        "seqPointMax",
+        "pcaData"
     })
-    public static class Tree {
+    public static class PcaViewer {
 
-        @XmlElement(namespace = "www.jalview.org")
+        @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;
-        @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 = "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")
@@ -3038,201 +3170,1266 @@ public class JalviewModel {
         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 title property.
+         * 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 }
+         * 
          * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
          */
-        public String getTitle() {
-            return title;
+        public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
+            if (sequencePoint == null) {
+                sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
+            }
+            return this.sequencePoint;
         }
 
         /**
-         * Sets the value of the title property.
+         * 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 }
+         * 
          * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
          */
-        public void setTitle(String value) {
-            this.title = value;
+        public List<JalviewModel.PcaViewer.Axis> getAxis() {
+            if (axis == null) {
+                axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
+            }
+            return this.axis;
         }
 
         /**
-         * Gets the value of the newick property.
+         * Gets the value of the seqPointMin property.
          * 
          * @return
          *     possible object is
-         *     {@link String }
+         *     {@link JalviewModel.PcaViewer.SeqPointMin }
          *     
          */
-        public String getNewick() {
-            return newick;
+        public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
+            return seqPointMin;
         }
 
         /**
-         * Sets the value of the newick property.
+         * Sets the value of the seqPointMin property.
          * 
          * @param value
          *     allowed object is
-         *     {@link String }
+         *     {@link JalviewModel.PcaViewer.SeqPointMin }
          *     
          */
-        public void setNewick(String value) {
-            this.newick = value;
+        public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
+            this.seqPointMin = value;
         }
 
         /**
-         * Gets the value of the fontName property.
+         * Gets the value of the seqPointMax property.
          * 
          * @return
          *     possible object is
-         *     {@link String }
+         *     {@link JalviewModel.PcaViewer.SeqPointMax }
          *     
          */
-        public String getFontName() {
-            return fontName;
+        public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
+            return seqPointMax;
         }
 
         /**
-         * Sets the value of the fontName property.
+         * Sets the value of the seqPointMax property.
          * 
          * @param value
          *     allowed object is
-         *     {@link String }
+         *     {@link JalviewModel.PcaViewer.SeqPointMax }
          *     
          */
-        public void setFontName(String value) {
-            this.fontName = value;
+        public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
+            this.seqPointMax = value;
         }
 
         /**
-         * Gets the value of the fontSize property.
+         * Gets the value of the pcaData property.
          * 
          * @return
          *     possible object is
-         *     {@link Integer }
+         *     {@link PcaDataType }
          *     
          */
-        public Integer getFontSize() {
-            return fontSize;
+        public PcaDataType getPcaData() {
+            return pcaData;
         }
 
         /**
-         * Sets the value of the fontSize property.
+         * Sets the value of the pcaData property.
          * 
          * @param value
          *     allowed object is
-         *     {@link Integer }
+         *     {@link PcaDataType }
          *     
          */
-        public void setFontSize(Integer value) {
-            this.fontSize = value;
+        public void setPcaData(PcaDataType value) {
+            this.pcaData = value;
         }
 
         /**
-         * Gets the value of the fontStyle property.
+         * Gets the value of the title property.
          * 
          * @return
          *     possible object is
-         *     {@link Integer }
+         *     {@link String }
          *     
          */
-        public Integer getFontStyle() {
-            return fontStyle;
+        public String getTitle() {
+            return title;
         }
 
         /**
-         * Sets the value of the fontStyle property.
+         * Sets the value of the title property.
          * 
          * @param value
          *     allowed object is
-         *     {@link Integer }
+         *     {@link String }
          *     
          */
-        public void setFontStyle(Integer value) {
-            this.fontStyle = value;
+        public void setTitle(String value) {
+            this.title = value;
         }
 
         /**
-         * Gets the value of the threshold property.
+         * Gets the value of the scoreModelName property.
          * 
          * @return
          *     possible object is
-         *     {@link Float }
+         *     {@link String }
          *     
          */
-        public Float getThreshold() {
-            return threshold;
+        public String getScoreModelName() {
+            return scoreModelName;
         }
 
         /**
-         * Sets the value of the threshold property.
+         * Sets the value of the scoreModelName property.
          * 
          * @param value
          *     allowed object is
-         *     {@link Float }
+         *     {@link String }
          *     
          */
-        public void setThreshold(Float value) {
-            this.threshold = value;
+        public void setScoreModelName(String value) {
+            this.scoreModelName = value;
         }
 
         /**
-         * Gets the value of the showBootstrap property.
+         * Gets the value of the xDim property.
          * 
          * @return
          *     possible object is
-         *     {@link Boolean }
+         *     {@link Integer }
          *     
          */
-        public Boolean isShowBootstrap() {
-            return showBootstrap;
+        public Integer getXDim() {
+            return xDim;
         }
 
         /**
-         * Sets the value of the showBootstrap property.
+         * Sets the value of the xDim property.
          * 
          * @param value
          *     allowed object is
-         *     {@link Boolean }
+         *     {@link Integer }
          *     
          */
-        public void setShowBootstrap(Boolean value) {
-            this.showBootstrap = value;
+        public void setXDim(Integer value) {
+            this.xDim = value;
         }
 
         /**
-         * Gets the value of the showDistances property.
+         * Gets the value of the yDim property.
          * 
          * @return
          *     possible object is
-         *     {@link Boolean }
+         *     {@link Integer }
          *     
          */
-        public Boolean isShowDistances() {
-            return showDistances;
+        public Integer getYDim() {
+            return yDim;
         }
 
         /**
-         * Sets the value of the showDistances property.
+         * Sets the value of the yDim property.
          * 
          * @param value
          *     allowed object is
-         *     {@link Boolean }
+         *     {@link Integer }
          *     
          */
-        public void setShowDistances(Boolean value) {
-            this.showDistances = value;
+        public void setYDim(Integer value) {
+            this.yDim = value;
         }
 
         /**
-         * Gets the value of the markUnlinked property.
+         * 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;
+        }
+
+        /**
+         * 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;
+        }
+
+        /**
+         * 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;
+        }
+
+        /**
+         * 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;
+        }
+
+        /**
+         * 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.
+         * 
+         * @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;
+        }
+
+        /**
+         * Gets the value of the includeGaps property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isIncludeGaps() {
+            return includeGaps;
+        }
+
+        /**
+         * Sets the value of the includeGaps property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setIncludeGaps(Boolean value) {
+            this.includeGaps = value;
+        }
+
+        /**
+         * Gets the value of the matchGaps property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isMatchGaps() {
+            return matchGaps;
+        }
+
+        /**
+         * Sets the value of the matchGaps property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setMatchGaps(Boolean value) {
+            this.matchGaps = value;
+        }
+
+        /**
+         * Gets the value of the includeGappedColumns property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isIncludeGappedColumns() {
+            return includeGappedColumns;
+        }
+
+        /**
+         * Sets the value of the includeGappedColumns property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setIncludeGappedColumns(Boolean value) {
+            this.includeGappedColumns = value;
+        }
+
+        /**
+         * Gets the value of the denominateByShortestLength property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isDenominateByShortestLength() {
+            return denominateByShortestLength;
+        }
+
+        /**
+         * Sets the value of the denominateByShortestLength property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setDenominateByShortestLength(Boolean value) {
+            this.denominateByShortestLength = 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 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;
+            }
+
+        }
+
+
+        /**
+         * <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;
+            }
+
+        }
+
+
+        /**
+         * <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;
+            }
+
+        }
+
+    }
+
+
+    /**
+     * <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;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *     &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 = "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 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
@@ -3328,6 +4525,34 @@ public class JalviewModel {
         }
 
         /**
+         * Gets the value of the linkToAllViews property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isLinkToAllViews() {
+            if (linkToAllViews == null) {
+                return false;
+            } else {
+                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
diff --git a/src/jalview/xml/binding/jalview/JalviewUserColours.java b/src/jalview/xml/binding/jalview/JalviewUserColours.java
index 0de2ac0..701647c 100644
--- a/src/jalview/xml/binding/jalview/JalviewUserColours.java
+++ b/src/jalview/xml/binding/jalview/JalviewUserColours.java
@@ -2,7 +2,7 @@
 // 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: 2018.09.28 at 12:18:54 PM BST 
+// Generated on: 2018.12.20 at 11:47:26 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/MapListType.java b/src/jalview/xml/binding/jalview/MapListType.java
index 345556f..3d7b5eb 100644
--- a/src/jalview/xml/binding/jalview/MapListType.java
+++ b/src/jalview/xml/binding/jalview/MapListType.java
@@ -2,7 +2,7 @@
 // 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: 2018.09.28 at 12:18:54 PM BST 
+// Generated on: 2018.12.20 at 11:47:26 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/Mapping.java b/src/jalview/xml/binding/jalview/Mapping.java
index cd82a2a..3cbebc0 100644
--- a/src/jalview/xml/binding/jalview/Mapping.java
+++ b/src/jalview/xml/binding/jalview/Mapping.java
@@ -2,7 +2,7 @@
 // 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: 2018.09.28 at 12:18:54 PM BST 
+// Generated on: 2018.12.20 at 11:47:26 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/NoValueColour.java b/src/jalview/xml/binding/jalview/NoValueColour.java
index 8fd65f0..15fc45d 100644
--- a/src/jalview/xml/binding/jalview/NoValueColour.java
+++ b/src/jalview/xml/binding/jalview/NoValueColour.java
@@ -2,7 +2,7 @@
 // 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: 2018.09.28 at 12:18:54 PM BST 
+// Generated on: 2018.12.20 at 11:47:26 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/ObjectFactory.java b/src/jalview/xml/binding/jalview/ObjectFactory.java
index 0903928..6858f07 100644
--- a/src/jalview/xml/binding/jalview/ObjectFactory.java
+++ b/src/jalview/xml/binding/jalview/ObjectFactory.java
@@ -2,7 +2,7 @@
 // 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: 2018.09.28 at 12:18:54 PM BST 
+// Generated on: 2018.12.20 at 11:47:26 AM GMT 
 //
 
 
@@ -131,6 +131,14 @@ public class ObjectFactory {
     }
 
     /**
+     * Create an instance of {@link JalviewModel.PcaViewer }
+     * 
+     */
+    public JalviewModel.PcaViewer createJalviewModelPcaViewer() {
+        return new JalviewModel.PcaViewer();
+    }
+
+    /**
      * Create an instance of {@link JalviewModel.Viewport }
      * 
      */
@@ -163,6 +171,14 @@ public class ObjectFactory {
     }
 
     /**
+     * Create an instance of {@link DoubleMatrix }
+     * 
+     */
+    public DoubleMatrix createDoubleMatrix() {
+        return new DoubleMatrix();
+    }
+
+    /**
      * Create an instance of {@link AnnotationColourScheme }
      * 
      */
@@ -171,6 +187,22 @@ public class ObjectFactory {
     }
 
     /**
+     * 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 }
      * 
      */
@@ -363,6 +395,38 @@ public class ObjectFactory {
     }
 
     /**
+     * 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 }
      * 
      */
diff --git a/src/jalview/xml/binding/jalview/PcaDataType.java b/src/jalview/xml/binding/jalview/PcaDataType.java
new file mode 100644
index 0000000..e8c7cf2
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/PcaDataType.java
@@ -0,0 +1,129 @@
+//
+// 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: 2018.12.20 at 11:47:26 AM GMT 
+//
+
+
+package jalview.xml.binding.jalview;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * 
+ * 				The results of a PCA calculation
+ * 			
+ * 
+ * <p>Java class for PcaDataType complex type.
+ * 
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * 
+ * <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;
+    @XmlElement(required = true)
+    protected DoubleMatrix eigenMatrix;
+
+    /**
+     * 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;
+    }
+
+    /**
+     * 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;
+    }
+
+    /**
+     * 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;
+    }
+
+}
diff --git a/src/jalview/xml/binding/jalview/Pdbentry.java b/src/jalview/xml/binding/jalview/Pdbentry.java
index 4accccd..843ea6c 100644
--- a/src/jalview/xml/binding/jalview/Pdbentry.java
+++ b/src/jalview/xml/binding/jalview/Pdbentry.java
@@ -2,7 +2,7 @@
 // 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: 2018.09.28 at 12:18:54 PM BST 
+// Generated on: 2018.12.20 at 11:47:26 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/Sequence.java b/src/jalview/xml/binding/jalview/Sequence.java
index 937142a..abb40c9 100644
--- a/src/jalview/xml/binding/jalview/Sequence.java
+++ b/src/jalview/xml/binding/jalview/Sequence.java
@@ -2,7 +2,7 @@
 // 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: 2018.09.28 at 12:18:54 PM BST 
+// Generated on: 2018.12.20 at 11:47:26 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/SequenceSet.java b/src/jalview/xml/binding/jalview/SequenceSet.java
index 7bd7c1e..0fc7771 100644
--- a/src/jalview/xml/binding/jalview/SequenceSet.java
+++ b/src/jalview/xml/binding/jalview/SequenceSet.java
@@ -2,7 +2,7 @@
 // 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: 2018.09.28 at 12:18:54 PM BST 
+// Generated on: 2018.12.20 at 11:47:26 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/SequenceType.java b/src/jalview/xml/binding/jalview/SequenceType.java
index 004119f..07b8c24 100644
--- a/src/jalview/xml/binding/jalview/SequenceType.java
+++ b/src/jalview/xml/binding/jalview/SequenceType.java
@@ -2,7 +2,7 @@
 // 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: 2018.09.28 at 12:18:54 PM BST 
+// Generated on: 2018.12.20 at 11:47:26 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/ThresholdType.java b/src/jalview/xml/binding/jalview/ThresholdType.java
index 7ec43c7..e8b7e28 100644
--- a/src/jalview/xml/binding/jalview/ThresholdType.java
+++ b/src/jalview/xml/binding/jalview/ThresholdType.java
@@ -2,7 +2,7 @@
 // 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: 2018.09.28 at 12:18:54 PM BST 
+// Generated on: 2018.12.20 at 11:47:26 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/VAMSAS.java b/src/jalview/xml/binding/jalview/VAMSAS.java
index 70799ea..1f68de9 100644
--- a/src/jalview/xml/binding/jalview/VAMSAS.java
+++ b/src/jalview/xml/binding/jalview/VAMSAS.java
@@ -2,7 +2,7 @@
 // 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: 2018.09.28 at 12:18:54 PM BST 
+// Generated on: 2018.12.20 at 11:47:26 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
index fea0324..c884556 100644
--- a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
+++ b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
@@ -2,7 +2,7 @@
 // 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: 2018.09.28 at 12:18:54 PM BST 
+// Generated on: 2018.12.20 at 11:47:26 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/package-info.java b/src/jalview/xml/binding/jalview/package-info.java
index 4235c64..bd6dc77 100644
--- a/src/jalview/xml/binding/jalview/package-info.java
+++ b/src/jalview/xml/binding/jalview/package-info.java
@@ -2,7 +2,7 @@
 // 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: 2018.09.28 at 12:18:54 PM BST 
+// Generated on: 2018.12.20 at 11:47:26 AM GMT 
 //
 
 @javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
-- 
1.7.10.2