From: Charles Ofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Fri, 5 Dec 2014 12:23:07 +0000 (+0000)
Subject: Change the Html export to utilize svg
X-Git-Tag: Jalview_2_9~121^2~2
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=cca50cb3aee94f3ed1a5e504d45b8d8b665f8c5b

Change the Html export to utilize svg
---

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 2a804ad..3180993 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -57,7 +57,7 @@ import jalview.io.AnnotationFile;
 import jalview.io.FeaturesFile;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
-import jalview.io.HTMLOutput;
+import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
@@ -379,7 +379,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
                 && Character.isDigit(evt.getKeyChar()))
         {
-          alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+          alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
         }
 
         switch (evt.getKeyCode())
@@ -397,7 +397,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.moveCursor(0, 1);
+            alignPanel.getSeqPanel().moveCursor(0, 1);
           }
           break;
 
@@ -408,7 +408,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.moveCursor(0, -1);
+            alignPanel.getSeqPanel().moveCursor(0, -1);
           }
 
           break;
@@ -416,11 +416,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         case KeyEvent.VK_LEFT:
           if (evt.isAltDown() || !viewport.cursorMode)
           {
-            slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
+            slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
           }
           else
           {
-            alignPanel.seqPanel.moveCursor(-1, 0);
+            alignPanel.getSeqPanel().moveCursor(-1, 0);
           }
 
           break;
@@ -428,18 +428,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         case KeyEvent.VK_RIGHT:
           if (evt.isAltDown() || !viewport.cursorMode)
           {
-            slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
+            slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
           }
           else
           {
-            alignPanel.seqPanel.moveCursor(1, 0);
+            alignPanel.getSeqPanel().moveCursor(1, 0);
           }
           break;
 
         case KeyEvent.VK_SPACE:
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
+            alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
                     || evt.isShiftDown() || evt.isAltDown());
           }
           break;
@@ -463,7 +463,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+            alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
                     || evt.isShiftDown() || evt.isAltDown());
           }
 
@@ -472,19 +472,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         case KeyEvent.VK_S:
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.setCursorRow();
+            alignPanel.getSeqPanel().setCursorRow();
           }
           break;
         case KeyEvent.VK_C:
           if (viewport.cursorMode && !evt.isControlDown())
           {
-            alignPanel.seqPanel.setCursorColumn();
+            alignPanel.getSeqPanel().setCursorColumn();
           }
           break;
         case KeyEvent.VK_P:
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.setCursorPosition();
+            alignPanel.getSeqPanel().setCursorPosition();
           }
           break;
 
@@ -492,20 +492,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         case KeyEvent.VK_COMMA:
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.setCursorRowAndColumn();
+            alignPanel.getSeqPanel().setCursorRowAndColumn();
           }
           break;
 
         case KeyEvent.VK_Q:
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.setSelectionAreaAtCursor(true);
+            alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
           }
           break;
         case KeyEvent.VK_M:
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.setSelectionAreaAtCursor(false);
+            alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
           }
           break;
 
@@ -516,10 +516,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   { (viewport.cursorMode ? "on" : "off") }));
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
-            alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+            alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
+            alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
           }
-          alignPanel.seqPanel.seqCanvas.repaint();
+          alignPanel.getSeqPanel().seqCanvas.repaint();
           break;
 
         case KeyEvent.VK_F1:
@@ -738,14 +738,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
     conservationMenuItem.setSelected(av.getConservationSelected());
     seqLimits.setSelected(av.getShowJVSuffix());
-    idRightAlign.setSelected(av.rightAlignIds);
+    idRightAlign.setSelected(av.isRightAlignIds());
     centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
     renderGapsMenuItem.setSelected(av.renderGaps);
     wrapMenuItem.setSelected(av.wrapAlignment);
     scaleAbove.setVisible(av.wrapAlignment);
     scaleLeft.setVisible(av.wrapAlignment);
     scaleRight.setVisible(av.wrapAlignment);
-    annotationPanelMenuItem.setState(av.showAnnotation);
+    annotationPanelMenuItem.setState(av.isShowAnnotation());
     /*
      * Show/hide annotations only enabled if annotation panel is shown
      */
@@ -896,7 +896,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   public FeatureRenderer getFeatureRenderer()
   {
-    return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+    return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
   }
 
   @Override
@@ -1227,9 +1227,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
-    new HTMLOutput(alignPanel,
-            alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
-            alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+    // new HTMLOutput(alignPanel,
+    // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(),
+    // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+    new HtmlSvgOutput(alignPanel);
   }
 
   public void createImageMap(File file, String image)
@@ -1296,7 +1297,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void exportAnnotations_actionPerformed(ActionEvent e)
   {
     new AnnotationExporter().exportAnnotations(alignPanel,
-            viewport.showAnnotation ? viewport.getAlignment()
+            viewport.isShowAnnotation() ? viewport.getAlignment()
                     .getAlignmentAnnotation() : null, viewport
                     .getAlignment().getGroups(), ((Alignment) viewport
                     .getAlignment()).alignmentProperties);
@@ -1622,7 +1623,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (viewport.cursorMode)
     {
       sg.add(viewport.getAlignment().getSequenceAt(
-              alignPanel.seqPanel.seqCanvas.cursorY));
+              alignPanel.getSeqPanel().seqCanvas.cursorY));
     }
     else if (viewport.getSelectionGroup() != null
             && viewport.getSelectionGroup().getSize() != viewport
@@ -1672,7 +1673,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       if (viewport.cursorMode)
       {
-        alignPanel.seqPanel.moveCursor(size, 0);
+        alignPanel.getSeqPanel().moveCursor(size, 0);
       }
       else
       {
@@ -1683,7 +1684,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       if (viewport.cursorMode)
       {
-        alignPanel.seqPanel.moveCursor(-size, 0);
+        alignPanel.getSeqPanel().moveCursor(-size, 0);
       }
       else
       {
@@ -2111,9 +2112,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
         // >>>This is a fix for the moment, until a better solution is
         // found!!<<<
-        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
+        af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
                 .transferSettings(
-                        alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+                        alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
 
         // TODO: maintain provenance of an alignment, rather than just make the
         // title a concatenation of operations.
@@ -2171,9 +2172,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       // >>>This is a fix for the moment, until a better solution is
       // found!!<<<
-      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
+      af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
               .transferSettings(
-                      alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+                      alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
 
       // TODO: maintain provenance of an alignment, rather than just make the
       // title a concatenation of operations.
@@ -2337,14 +2338,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     if (viewport.cursorMode)
     {
-      alignPanel.seqPanel.keyboardNo1 = null;
-      alignPanel.seqPanel.keyboardNo2 = null;
+      alignPanel.getSeqPanel().keyboardNo1 = null;
+      alignPanel.getSeqPanel().keyboardNo2 = null;
     }
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
-    alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
-    alignPanel.idPanel.idCanvas.searchResults = null;
+    alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
+    alignPanel.getIdPanel().getIdCanvas().searchResults = null;
     alignPanel.paintAlignment(true);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
@@ -2745,7 +2746,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.setShowJVSuffix(seqLimits.isSelected());
 
-    alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
+    alignPanel.getIdPanel().getIdCanvas().setPreferredSize(alignPanel
             .calculateIdWidth());
     alignPanel.paintAlignment(true);
   }
@@ -2753,7 +2754,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void idRightAlign_actionPerformed(ActionEvent e)
   {
-    viewport.rightAlignIds = idRightAlign.isSelected();
+    viewport.setRightAlignIds(idRightAlign.isSelected());
     alignPanel.paintAlignment(true);
   }
 
@@ -2775,7 +2776,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (viewport.followHighlight = this.followHighlightMenuItem.getState())
     {
       alignPanel.scrollToPosition(
-              alignPanel.seqPanel.seqCanvas.searchResults, false);
+              alignPanel.getSeqPanel().seqCanvas.searchResults, false);
     }
   }
 
@@ -4882,7 +4883,7 @@ this,
     try
     {
       featuresFile = new FeaturesFile(file, type).parse(viewport
-              .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
+              .getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas
               .getFeatureRenderer().featureColours, false,
               jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
     } catch (Exception ex)
@@ -4894,10 +4895,10 @@ this,
     {
       viewport.showSequenceFeatures = true;
       showSeqFeatures.setSelected(true);
-      if (alignPanel.seqPanel.seqCanvas.fr != null)
+      if (alignPanel.getSeqPanel().seqCanvas.fr != null)
       {
         // update the min/max ranges where necessary
-        alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
+        alignPanel.getSeqPanel().seqCanvas.fr.findAllFeatures(true);
       }
       if (featureSettings != null)
       {
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index d24f6c4..40f95e2 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -97,7 +97,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   boolean showSequenceFeatures = false;
 
-  boolean showAnnotation = true;
+  private boolean showAnnotation = true;
 
   SequenceAnnotationOrder sortAnnotationsBy = null;
 
@@ -149,7 +149,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   Color textColour2 = Color.white;
 
-  boolean rightAlignIds = false;
+  private boolean rightAlignIds = false;
 
   /**
    * Creates a new AlignViewport object.
@@ -286,9 +286,9 @@ public class AlignViewport extends AlignmentViewport implements
     antiAlias = Cache.getDefault("ANTI_ALIAS", false);
 
     showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
-    showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
+    setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
 
-    rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
+    setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
     centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
     autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
 
@@ -839,7 +839,7 @@ public class AlignViewport extends AlignmentViewport implements
    */
   public boolean getShowAnnotation()
   {
-    return showAnnotation;
+    return isShowAnnotation();
   }
 
   /**
@@ -1293,4 +1293,19 @@ public class AlignViewport extends AlignmentViewport implements
   {
     this.showAutocalculatedAbove = showAutocalculatedAbove;
   }
+
+  public boolean isShowAnnotation()
+  {
+    return showAnnotation;
+  }
+
+  public boolean isRightAlignIds()
+  {
+    return rightAlignIds;
+  }
+
+  public void setRightAlignIds(boolean rightAlignIds)
+  {
+    this.rightAlignIds = rightAlignIds;
+  }
 }
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 5527f1e..e4a4c90 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -29,6 +29,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.jbgui.GAlignmentPanel;
+import jalview.math.AlignmentDimension;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
@@ -66,20 +67,21 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   OverviewPanel overviewPanel;
 
-  SeqPanel seqPanel;
+  private SeqPanel seqPanel;
 
-  IdPanel idPanel;
+  private IdPanel idPanel;
 
+  private boolean headless;
   IdwidthAdjuster idwidthAdjuster;
 
   /** DOCUMENT ME!! */
   public AlignFrame alignFrame;
 
-  ScalePanel scalePanel;
+  private ScalePanel scalePanel;
 
-  AnnotationPanel annotationPanel;
+  private AnnotationPanel annotationPanel;
 
-  AnnotationLabels alabels;
+  private AnnotationLabels alabels;
 
   // this value is set false when selection area being dragged
   boolean fastPaint = true;
@@ -100,23 +102,23 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     alignFrame = af;
     this.av = av;
-    seqPanel = new SeqPanel(av, this);
-    idPanel = new IdPanel(av, this);
+    setSeqPanel(new SeqPanel(av, this));
+    setIdPanel(new IdPanel(av, this));
 
-    scalePanel = new ScalePanel(av, this);
+    setScalePanel(new ScalePanel(av, this));
 
-    idPanelHolder.add(idPanel, BorderLayout.CENTER);
+    idPanelHolder.add(getIdPanel(), BorderLayout.CENTER);
     idwidthAdjuster = new IdwidthAdjuster(this);
     idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
 
-    annotationPanel = new AnnotationPanel(this);
-    alabels = new AnnotationLabels(this);
+    setAnnotationPanel(new AnnotationPanel(this));
+    setAlabels(new AnnotationLabels(this));
 
-    annotationScroller.setViewportView(annotationPanel);
-    annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
+    annotationScroller.setViewportView(getAnnotationPanel());
+    annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER);
 
-    scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
-    seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
+    scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER);
+    seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER);
 
     setScrollValues(0, 0);
 
@@ -166,13 +168,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
     idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av.charHeight
             + fm.getDescent()));
 
-    idPanel.idCanvas.gg = null;
-    seqPanel.seqCanvas.img = null;
-    annotationPanel.adjustPanelHeight();
+    getIdPanel().getIdCanvas().gg = null;
+    getSeqPanel().seqCanvas.img = null;
+    getAnnotationPanel().adjustPanelHeight();
 
     Dimension d = calculateIdWidth();
     d.setSize(d.width + 4, d.height);
-    idPanel.idCanvas.setPreferredSize(d);
+    getIdPanel().getIdCanvas().setPreferredSize(d);
     hscrollFillerPanel.setPreferredSize(d);
 
     if (overviewPanel != null)
@@ -240,7 +242,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     if (al.getAlignmentAnnotation() != null)
     {
-      fm = c.getFontMetrics(alabels.getFont());
+      fm = c.getFontMetrics(getAlabels().getFont());
 
       while (i < al.getAlignmentAnnotation().length)
       {
@@ -266,7 +268,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   public void highlightSearchResults(SearchResults results)
   {
     scrollToPosition(results);
-    seqPanel.seqCanvas.highlightSearchResults(results);
+    getSeqPanel().seqCanvas.highlightSearchResults(results);
   }
 
   /**
@@ -371,8 +373,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   void scrollToWrappedVisible(int res)
   {
-    int cwidth = seqPanel.seqCanvas
-            .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+    int cwidth = getSeqPanel().seqCanvas
+            .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
     if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth))
     {
       vscroll.setValue((res / cwidth));
@@ -441,7 +443,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   protected void validateAnnotationDimensions(boolean adjustPanelHeight)
   {
-    int height = annotationPanel.adjustPanelHeight();
+    int height = getAnnotationPanel().adjustPanelHeight();
 
     int theight = av.getCharHeight()
             * (av.getAlignment().getHeight() + (!av.hasHiddenRows() ? 0
@@ -503,7 +505,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       annotationScroller.setVisible(false);
       annotationSpaceFillerHolder.setVisible(false);
     }
-    else if (av.showAnnotation)
+    else if (av.isShowAnnotation())
     {
       annotationScroller.setVisible(true);
       annotationSpaceFillerHolder.setVisible(true);
@@ -603,10 +605,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
       width = av.getColumnSelection().findColumnPosition(width);
     }
 
-    av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1);
+    av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av.charWidth)) - 1);
 
-    hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
-    vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
+    hextent = getSeqPanel().seqCanvas.getWidth() / av.charWidth;
+    vextent = getSeqPanel().seqCanvas.getHeight() / av.charHeight;
 
     if (hextent > width)
     {
@@ -658,7 +660,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       int x = hscroll.getValue();
       av.setStartRes(x);
-      av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
+      av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av.getCharWidth())) - 1);
     }
 
     if (evt.getSource() == vscroll)
@@ -669,8 +671,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         if (offy > -1)
         {
-          int rowSize = seqPanel.seqCanvas
-                  .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+          int rowSize = getSeqPanel().seqCanvas
+                  .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
           av.setStartRes(offy * rowSize);
           av.setEndRes((offy + 1) * rowSize);
         }
@@ -692,7 +694,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         av.setStartSeq(offy);
         av.setEndSeq(offy
-                + (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
+                + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight()));
       }
     }
 
@@ -723,13 +725,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
       if (scrollX != 0 || scrollY != 0)
       {
-        idPanel.idCanvas.fastPaint(scrollY);
-        seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
-        scalePanel.repaint();
+        getIdPanel().getIdCanvas().fastPaint(scrollY);
+        getSeqPanel().seqCanvas.fastPaint(scrollX, scrollY);
+        getScalePanel().repaint();
 
         if (av.getShowAnnotation() && scrollX != 0)
         {
-          annotationPanel.fastPaint(scrollX);
+          getAnnotationPanel().fastPaint(scrollX);
         }
       }
     }
@@ -769,7 +771,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     invalidate();
 
-    Dimension d = idPanel.idCanvas.getPreferredSize();
+    Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
     idPanelHolder.setPreferredSize(d);
     hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
     validate();
@@ -783,13 +785,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
         maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
       }
 
-      int canvasWidth = seqPanel.seqCanvas
-              .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+      int canvasWidth = getSeqPanel().seqCanvas
+              .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
       if (canvasWidth > 0)
       {
         int max = maxwidth
-                / seqPanel.seqCanvas
-                        .getWrappedCanvasWidth(seqPanel.seqCanvas
+                / getSeqPanel().seqCanvas
+                        .getWrappedCanvasWidth(getSeqPanel().seqCanvas
                                 .getWidth()) + 1;
         vscroll.setMaximum(max);
         vscroll.setUnitIncrement(1);
@@ -905,9 +907,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1)
             * pheight;
 
-    if (av.showAnnotation)
+    if (av.isShowAnnotation())
     {
-      pagesHigh += annotationPanel.adjustPanelHeight() + 3;
+      pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
     }
 
     pagesHigh /= pheight;
@@ -919,7 +921,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     // draw Scale
     pg.translate(idWidth, 0);
-    scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth,
+    getScalePanel().drawScale(pg, startRes, endRes, pwidth - idWidth,
             scaleHeight);
     pg.translate(-idWidth, scaleHeight);
 
@@ -928,7 +930,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     Color currentColor = null;
     Color currentTextColor = null;
 
-    pg.setFont(idPanel.idCanvas.idfont);
+    pg.setFont(getIdPanel().getIdCanvas().getIdfont());
 
     SequenceI seq;
     for (int i = startSeq; i < endSeq; i++)
@@ -953,7 +955,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       pg.setColor(currentTextColor);
 
       int xPos = 0;
-      if (av.rightAlignIds)
+      if (av.isRightAlignIds())
       {
         fm = pg.getFontMetrics();
         xPos = idWidth
@@ -972,17 +974,17 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     // draw main sequence panel
     pg.translate(idWidth, 0);
-    seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
+    getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
 
-    if (av.showAnnotation && (endSeq == av.getAlignment().getHeight()))
+    if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight()))
     {
       // draw annotation - need to offset for current scroll position
-      int offset = -alabels.scrollOffset;
+      int offset = -getAlabels().getScrollOffset();
       pg.translate(0, offset);
       pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
-      alabels.drawComponent(pg, idWidth);
+      getAlabels().drawComponent(pg, idWidth);
       pg.translate(idWidth + 3, 0);
-      annotationPanel.renderer.drawComponent(annotationPanel, av,
+      getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
               pg, -1, startRes, endRes + 1);
       pg.translate(0, -offset);
     }
@@ -1013,9 +1015,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     int annotationHeight = 0;
     AnnotationLabels labels = null;
-    if (av.showAnnotation)
+    if (av.isShowAnnotation())
     {
-      annotationHeight = annotationPanel.adjustPanelHeight();
+      annotationHeight = getAnnotationPanel().adjustPanelHeight();
       labels = new AnnotationLabels(av);
     }
 
@@ -1036,7 +1038,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
     }
 
-    int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth
+    int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth
             - idWidth);
 
     int totalHeight = cHeight * (maxwidth / resWidth + 1);
@@ -1059,11 +1061,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       for (int i = 0; i < av.getAlignment().getHeight(); i++)
       {
-        pg.setFont(idPanel.idCanvas.idfont);
+        pg.setFont(getIdPanel().getIdCanvas().getIdfont());
         SequenceI s = av.getAlignment().getSequenceAt(i);
         String string = s.getDisplayId(av.getShowJVSuffix());
         int xPos = 0;
-        if (av.rightAlignIds)
+        if (av.isRightAlignIds())
         {
           FontMetrics fm = pg.getFontMetrics();
           xPos = idWidth - fm.stringWidth(string) - 4;
@@ -1088,7 +1090,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     pg.translate(idWidth, 0);
 
-    seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight,
+    getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight,
             0);
 
     if ((pi * pheight) < totalHeight)
@@ -1108,7 +1110,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * 
    * @return
    */
-  int getVisibleIdWidth()
+  public int getVisibleIdWidth()
   {
     return getVisibleIdWidth(true);
   }
@@ -1122,7 +1124,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    *          be returned
    * @return
    */
-  int getVisibleIdWidth(boolean onscreen)
+  public int getVisibleIdWidth(boolean onscreen)
   {
     // see if rendering offscreen - check preferences and calc width accordingly
     if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
@@ -1133,7 +1135,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (onscreen
             || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
     {
-      return (idPanel.getWidth() > 0 ? idPanel.getWidth()
+      return (getIdPanel().getWidth() > 0 ? getIdPanel().getWidth()
               : calculateIdWidth().width + 4);
     }
     return idwidth.intValue() + 4;
@@ -1142,7 +1144,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
   {
     long progress = System.currentTimeMillis();
-    boolean headless = (System.getProperty("java.awt.headless") != null && System
+    headless = (System.getProperty("java.awt.headless") != null && System
             .getProperty("java.awt.headless").equals("true"));
     if (alignFrame != null && !headless)
     {
@@ -1153,44 +1155,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     try
     {
-      int maxwidth = av.getAlignment().getWidth();
-      if (av.hasHiddenColumns())
-      {
-        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
-      }
-
-      int height = ((av.getAlignment().getHeight() + 1) * av.charHeight)
-              + scalePanel.getHeight();
-      int width = getVisibleIdWidth(false) + (maxwidth * av.charWidth);
-
-      if (av.getWrapAlignment())
-      {
-        height = getWrappedHeight();
-        if (headless)
-        {
-          // need to obtain default alignment width and then add in any
-          // additional allowance for id margin
-          // this duplicates the calculation in getWrappedHeight but adjusts for
-          // offscreen idWith
-          width = alignFrame.getWidth() - vscroll.getPreferredSize().width
-                  - alignFrame.getInsets().left
-                  - alignFrame.getInsets().right - getVisibleIdWidth()
-                  + getVisibleIdWidth(false);
-        }
-        else
-        {
-          width = seqPanel.getWidth() + getVisibleIdWidth(false);
-        }
-
-      }
-      else if (av.getShowAnnotation())
-      {
-        height += annotationPanel.adjustPanelHeight() + 3;
-      }
-
+      AlignmentDimension aDimension = getAlignmentDimension();
       try
       {
-
         jalview.util.ImageMaker im;
         final String imageAction, imageTitle;
         if (type == jalview.util.ImageMaker.TYPE.PNG)
@@ -1209,13 +1176,15 @@ public class AlignmentPanel extends GAlignmentPanel implements
           imageTitle = alignFrame.getTitle();
         }
 
-        im = new jalview.util.ImageMaker(this, type, imageAction, width,
-                height, file, imageTitle);
+        im = new jalview.util.ImageMaker(this, type, imageAction,
+                aDimension.getWidth(), aDimension.getHeight(), file,
+                imageTitle);
         if (av.getWrapAlignment())
         {
           if (im.getGraphics() != null)
           {
-            printWrappedAlignment(im.getGraphics(), width, height, 0);
+            printWrappedAlignment(im.getGraphics(), aDimension.getWidth(),
+                    aDimension.getHeight(), 0);
             im.writeImage();
           }
         }
@@ -1223,7 +1192,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
         {
           if (im.getGraphics() != null)
           {
-            printUnwrapped(im.getGraphics(), width, height, 0);
+            printUnwrapped(im.getGraphics(), aDimension.getWidth(),
+                    aDimension.getHeight(), 0);
             im.writeImage();
           }
         }
@@ -1247,6 +1217,46 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
   }
 
+  public AlignmentDimension getAlignmentDimension()
+  {
+    int maxwidth = av.getAlignment().getWidth();
+    if (av.hasHiddenColumns())
+    {
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
+    }
+
+    int height = ((av.getAlignment().getHeight() + 1) * av.charHeight)
+            + getScalePanel().getHeight();
+    int width = getVisibleIdWidth(false) + (maxwidth * av.charWidth);
+
+    if (av.getWrapAlignment())
+    {
+      height = getWrappedHeight();
+      if (headless)
+      {
+        // need to obtain default alignment width and then add in any
+        // additional allowance for id margin
+        // this duplicates the calculation in getWrappedHeight but adjusts for
+        // offscreen idWith
+        width = alignFrame.getWidth() - vscroll.getPreferredSize().width
+                - alignFrame.getInsets().left
+                - alignFrame.getInsets().right - getVisibleIdWidth()
+                + getVisibleIdWidth(false);
+      }
+      else
+      {
+        width = getSeqPanel().getWidth() + getVisibleIdWidth(false);
+      }
+
+    }
+    else if (av.getShowAnnotation())
+    {
+      height += getAnnotationPanel().adjustPanelHeight() + 3;
+    }
+    return new AlignmentDimension(width, height);
+
+  }
+
   /**
    * DOCUMENT ME!
    */
@@ -1410,7 +1420,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   int getWrappedHeight()
   {
-    int seqPanelWidth = seqPanel.seqCanvas.getWidth();
+    int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
 
     if (System.getProperty("java.awt.headless") != null
             && System.getProperty("java.awt.headless").equals("true"))
@@ -1420,7 +1430,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
               - alignFrame.getInsets().left - alignFrame.getInsets().right;
     }
 
-    int chunkWidth = seqPanel.seqCanvas
+    int chunkWidth = getSeqPanel().seqCanvas
             .getWrappedCanvasWidth(seqPanelWidth);
 
     int hgap = av.charHeight;
@@ -1430,9 +1440,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
 
     int annotationHeight = 0;
-    if (av.showAnnotation)
+    if (av.isShowAnnotation())
     {
-      annotationHeight = annotationPanel.adjustPanelHeight();
+      annotationHeight = getAnnotationPanel().adjustPanelHeight();
     }
 
     int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
@@ -1455,15 +1465,15 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public void closePanel()
   {
-    PaintRefresher.RemoveComponent(seqPanel.seqCanvas);
-    PaintRefresher.RemoveComponent(idPanel.idCanvas);
+    PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
+    PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
     PaintRefresher.RemoveComponent(this);
     if (av != null)
     {
       jalview.structure.StructureSelectionManager ssm = av
               .getStructureSelectionManager();
-      ssm.removeStructureViewerListener(seqPanel, null);
-      ssm.removeSelectionListener(seqPanel);
+      ssm.removeStructureViewerListener(getSeqPanel(), null);
+      ssm.removeSelectionListener(getSeqPanel());
       av.setAlignment(null);
       av = null;
     }
@@ -1554,14 +1564,64 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   public void updateFeatureRenderer(FeatureRenderer fr)
   {
-    fr.transferSettings(seqPanel.seqCanvas.getFeatureRenderer());
+    fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
   }
 
   public void updateFeatureRendererFrom(FeatureRenderer fr)
   {
-    if (seqPanel.seqCanvas.getFeatureRenderer() != null)
+    if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
     {
-      seqPanel.seqCanvas.getFeatureRenderer().transferSettings(fr);
+      getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr);
     }
   }
+
+  public ScalePanel getScalePanel()
+  {
+    return scalePanel;
+  }
+
+  public void setScalePanel(ScalePanel scalePanel)
+  {
+    this.scalePanel = scalePanel;
+  }
+
+  public SeqPanel getSeqPanel()
+  {
+    return seqPanel;
+  }
+
+  public void setSeqPanel(SeqPanel seqPanel)
+  {
+    this.seqPanel = seqPanel;
+  }
+
+  public AnnotationPanel getAnnotationPanel()
+  {
+    return annotationPanel;
+  }
+
+  public void setAnnotationPanel(AnnotationPanel annotationPanel)
+  {
+    this.annotationPanel = annotationPanel;
+  }
+
+  public AnnotationLabels getAlabels()
+  {
+    return alabels;
+  }
+
+  public void setAlabels(AnnotationLabels alabels)
+  {
+    this.alabels = alabels;
+  }
+
+  public IdPanel getIdPanel()
+  {
+    return idPanel;
+  }
+
+  public void setIdPanel(IdPanel idPanel)
+  {
+    this.idPanel = idPanel;
+  }
 }
diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 315c3e2..c68b2b1 100644
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -215,7 +215,7 @@ public class AnnotationExporter extends JPanel
       return fcols;
     }
     Enumeration en = ap.av.featuresDisplayed.keys();
-    FeatureRenderer fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); // consider
+    FeatureRenderer fr = ap.getSeqPanel().seqCanvas.getFeatureRenderer(); // consider
                                                                      // higher
                                                                      // level
                                                                      // method ?
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 6e8417f..501df8a 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -99,7 +99,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
   int selectedRow;
 
-  int scrollOffset = 0;
+  private int scrollOffset = 0;
 
   Font font = new Font("Arial", Font.PLAIN, 11);
 
@@ -143,7 +143,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
     addMouseListener(this);
     addMouseMotionListener(this);
-    addMouseWheelListener(ap.annotationPanel);
+    addMouseWheelListener(ap.getAnnotationPanel());
   }
 
   public AnnotationLabels(AlignViewport av)
@@ -325,7 +325,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    */
   public void mousePressed(MouseEvent evt)
   {
-    getSelectedRow(evt.getY() - scrollOffset);
+    getSelectedRow(evt.getY() - getScrollOffset());
     oldY = evt.getY();
   }
 
@@ -338,7 +338,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
   public void mouseReleased(MouseEvent evt)
   {
     int start = selectedRow;
-    getSelectedRow(evt.getY() - scrollOffset);
+    getSelectedRow(evt.getY() - getScrollOffset());
     int end = selectedRow;
 
     if (start != end)
@@ -360,7 +360,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     resizePanel = false;
     dragEvent = null;
     repaint();
-    ap.annotationPanel.repaint();
+    ap.getAnnotationPanel().repaint();
   }
 
   /**
@@ -439,7 +439,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
   {
     resizePanel = evt.getY() < 10;
 
-    getSelectedRow(evt.getY() - scrollOffset);
+    getSelectedRow(evt.getY() - getScrollOffset());
 
     if (selectedRow > -1
             && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow)
@@ -533,7 +533,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           {
             // todo: make the ap scroll to the selection - not necessary, first
             // click highlights/scrolls, second selects
-            ap.seqPanel.ap.idPanel.highlightSearchResults(null);
+            ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
             ap.av.setSelectionGroup(// new SequenceGroup(
             aa[selectedRow].groupRef); // );
             ap.paintAlignment(false);
@@ -542,7 +542,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           }
           else
           {
-            ap.seqPanel.ap.idPanel
+            ap.getSeqPanel().ap.getIdPanel()
                     .highlightSearchResults(aa[selectedRow].groupRef
                             .getSequences(null));
           }
@@ -552,13 +552,13 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         {
           if (evt.getClickCount() == 1)
           {
-            ap.seqPanel.ap.idPanel.highlightSearchResults(Arrays
+            ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(Arrays
                     .asList(new SequenceI[]
                     { aa[selectedRow].sequenceRef }));
           }
           else if (evt.getClickCount() >= 2)
           {
-            ap.seqPanel.ap.idPanel.highlightSearchResults(null);
+            ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
             SequenceGroup sg = ap.av.getSelectionGroup();
             if (sg!=null)
             {
@@ -696,7 +696,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             {
               // TODO: pass on reference to ap so the view can be updated.
               aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
-              ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+              ap.getAnnotationPanel().paint(ap.getAnnotationPanel().getGraphics());
             }
             else
             {
@@ -962,7 +962,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     g.setColor(Color.white);
     g.fillRect(0, 0, getWidth(), getHeight());
 
-    g.translate(0, scrollOffset);
+    g.translate(0, getScrollOffset());
     g.setColor(Color.black);
 
     AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
@@ -976,7 +976,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     int ofontH = fontHeight;
     int sOffset = 0;
     int visHeight = 0;
-    int[] visr = (ap != null && ap.annotationPanel != null) ? ap.annotationPanel
+    int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap.getAnnotationPanel()
             .getVisibleVRange() : null;
     if (clip && visr != null)
     {
@@ -1116,13 +1116,13 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
     if (resizePanel)
     {
-      g.drawImage(image, 2, 0 - scrollOffset, this);
+      g.drawImage(image, 2, 0 - getScrollOffset(), this);
     }
     else if (dragEvent != null && aa != null)
     {
       g.setColor(Color.lightGray);
       g.drawString(aa[selectedRow].label, dragEvent.getX(),
-              dragEvent.getY() - scrollOffset);
+              dragEvent.getY() - getScrollOffset());
     }
 
     if (!av.wrapAlignment && ((aa == null) || (aa.length < 1)))
@@ -1132,4 +1132,9 @@ public class AnnotationLabels extends JPanel implements MouseListener,
               18);
     }
   }
+
+  public int getScrollOffset()
+  {
+    return scrollOffset;
+  }
 }
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 9f56206..3a97f96 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -241,7 +241,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     // update annotation label display
-    ap.alabels.setScrollOffset(-evt.getValue());
+    ap.getAlabels().setScrollOffset(-evt.getValue());
   }
 
   /**
@@ -566,7 +566,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       return;
     }
 
-    ap.scalePanel.mousePressed(evt);
+    ap.getScalePanel().mousePressed(evt);
 
   }
 
@@ -582,7 +582,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     graphStretch = -1;
     graphStretchY = -1;
     mouseDragging = false;
-    ap.scalePanel.mouseReleased(evt);
+    ap.getScalePanel().mouseReleased(evt);
   }
 
   /**
@@ -594,7 +594,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public void mouseEntered(MouseEvent evt)
   {
-    ap.scalePanel.mouseEntered(evt);
+    ap.getScalePanel().mouseEntered(evt);
   }
 
   /**
@@ -606,7 +606,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public void mouseExited(MouseEvent evt)
   {
-    ap.scalePanel.mouseExited(evt);
+    ap.getScalePanel().mouseExited(evt);
   }
 
   /**
@@ -632,7 +632,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     }
     else
     {
-      ap.scalePanel.mouseDragged(evt);
+      ap.getScalePanel().mouseDragged(evt);
     }
   }
 
@@ -809,7 +809,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     {
       try
       {
-        image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
+        image = new BufferedImage(imgWidth, ap.getAnnotationPanel().getHeight(),
                 BufferedImage.TYPE_INT_RGB);
       } catch (OutOfMemoryError oom)
       {
@@ -1013,9 +1013,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public int[] getVisibleVRange()
   {
-    if (ap != null && ap.alabels != null)
+    if (ap != null && ap.getAlabels() != null)
     {
-      int sOffset = -ap.alabels.scrollOffset;
+      int sOffset = -ap.getAlabels().getScrollOffset();
       int visHeight = sOffset + ap.annotationSpaceFillerHolder.getHeight();
       bounds[0] = sOffset;
       bounds[1] = visHeight;
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index fcb31eb..4dfd18a 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -315,9 +315,9 @@ public class AppJmol extends GStructureViewer implements Runnable,
         // TODO : Fix multiple seq to one chain issue here.
         ap.getStructureSelectionManager().setMapping(seq, chains,
                 alreadyMapped, AppletFormatAdapter.FILE);
-        if (ap.seqPanel.seqCanvas.fr != null)
+        if (ap.getSeqPanel().seqCanvas.fr != null)
         {
-          ap.seqPanel.seqCanvas.fr.featuresAdded();
+          ap.getSeqPanel().seqCanvas.fr.featuresAdded();
           ap.paintAlignment(true);
         }
 
diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 02865e1..2f84d28 100644
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -244,9 +244,9 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable,
         // TODO : Fix multiple seq to one chain issue here.
         ap.getStructureSelectionManager().setMapping(seq, chains,
                 alreadyMapped, AppletFormatAdapter.FILE);
-        if (ap.seqPanel.seqCanvas.fr != null)
+        if (ap.getSeqPanel().seqCanvas.fr != null)
         {
-          ap.seqPanel.seqCanvas.fr.featuresAdded();
+          ap.getSeqPanel().seqCanvas.fr.featuresAdded();
           ap.paintAlignment(true);
         }
 
diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index d2d9c9c..cbdf2ef 100644
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -84,10 +84,10 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
   {
     this.ap = ap;
     this.av = ap.av;
-    if (ap != null && ap.seqPanel != null && ap.seqPanel.seqCanvas != null
-            && ap.seqPanel.seqCanvas.fr != null)
+    if (ap != null && ap.getSeqPanel() != null && ap.getSeqPanel().seqCanvas != null
+            && ap.getSeqPanel().seqCanvas.fr != null)
     {
-      transferSettings(ap.seqPanel.seqCanvas.fr);
+      transferSettings(ap.getSeqPanel().seqCanvas.fr);
     }
   }
 
@@ -1095,7 +1095,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
             highlight.addResult(sequences[0], features[index].getBegin(),
                     features[index].getEnd());
 
-            ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
+            ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
 
           }
           Object col = getFeatureStyle(name.getText());
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 2210148..9748f42 100644
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -527,7 +527,7 @@ public class FeatureSettings extends JPanel
       {
         fr.featureGroups.put(check.getText(),
                 new Boolean(check.isSelected()));
-        af.alignPanel.seqPanel.seqCanvas.repaint();
+        af.alignPanel.getSeqPanel().seqCanvas.repaint();
         if (af.alignPanel.overviewPanel != null)
         {
           af.alignPanel.overviewPanel.updateOverviewImage();
diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 8eddc06..acdaf92 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -182,7 +182,7 @@ public class Finder extends GFinder
               searchResults.getResultEnd(i), "Search Results");
     }
 
-    if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+    if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
             features, true, ap))
     {
       ap.alignFrame.showSeqFeatures.setSelected(true);
@@ -229,11 +229,11 @@ public class Finder extends GFinder
     if ((idMatch.size() > 0))
     {
       haveResults = true;
-      ap.idPanel.highlightSearchResults(idMatch);
+      ap.getIdPanel().highlightSearchResults(idMatch);
     }
     else
     {
-      ap.idPanel.highlightSearchResults(null);
+      ap.getIdPanel().highlightSearchResults(null);
     }
 
     if (searchResults.getSize() > 0)
diff --git a/src/jalview/gui/FontChooser.java b/src/jalview/gui/FontChooser.java
index b6116d9..36e4c52 100755
--- a/src/jalview/gui/FontChooser.java
+++ b/src/jalview/gui/FontChooser.java
@@ -129,7 +129,7 @@ public class FontChooser extends GFontChooser
   public void smoothFont_actionPerformed(ActionEvent e)
   {
     ap.av.antiAlias = smoothFont.isSelected();
-    ap.annotationPanel.image = null;
+    ap.getAnnotationPanel().image = null;
     ap.paintAlignment(true);
   }
 
diff --git a/src/jalview/gui/HTMLOptions.java b/src/jalview/gui/HTMLOptions.java
new file mode 100644
index 0000000..0ef4710
--- /dev/null
+++ b/src/jalview/gui/HTMLOptions.java
@@ -0,0 +1,143 @@
+package jalview.gui;
+
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.BorderFactory;
+import javax.swing.ButtonGroup;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JRadioButton;
+
+public class HTMLOptions extends JPanel
+{
+  JDialog dialog;
+
+  public boolean cancelled = false;
+
+  String value;
+
+  public HTMLOptions()
+  {
+    try
+    {
+      jbInit();
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+
+    ButtonGroup bg = new ButtonGroup();
+    bg.add(lineart);
+    bg.add(text);
+
+    JOptionPane pane = new JOptionPane(null, JOptionPane.DEFAULT_OPTION,
+            JOptionPane.DEFAULT_OPTION, null, new Object[]
+            { this });
+
+    dialog = pane.createDialog(Desktop.desktop, "HTML Rendering options");
+    dialog.setVisible(true);
+
+  }
+
+  private void jbInit() throws Exception
+  {
+    lineart.setFont(JvSwingUtils.getLabelFont());
+    lineart.setText(MessageManager.getString("label.lineart"));
+    text.setFont(JvSwingUtils.getLabelFont());
+    text.setText(MessageManager.getString("action.text"));
+    text.setSelected(true);
+    askAgain.setFont(JvSwingUtils.getLabelFont());
+    askAgain.setText(MessageManager.getString("label.dont_ask_me_again"));
+    ok.setText(MessageManager.getString("action.ok"));
+    ok.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        ok_actionPerformed(e);
+      }
+    });
+    cancel.setText(MessageManager.getString("action.cancel"));
+    cancel.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        cancel_actionPerformed(e);
+      }
+    });
+    jLabel1.setFont(JvSwingUtils.getLabelFont());
+    jLabel1.setText("Select HTML character rendering style");
+    this.setLayout(borderLayout1);
+    jPanel3.setBorder(BorderFactory.createEtchedBorder());
+    jPanel2.add(text);
+    jPanel2.add(lineart);
+    jPanel2.add(askAgain);
+    jPanel1.add(ok);
+    jPanel1.add(cancel);
+    jPanel3.add(jLabel1);
+    jPanel3.add(jPanel2);
+    this.add(jPanel3, java.awt.BorderLayout.CENTER);
+    this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+  }
+
+  JRadioButton lineart = new JRadioButton();
+
+  JRadioButton text = new JRadioButton();
+
+  JCheckBox askAgain = new JCheckBox();
+
+  JButton ok = new JButton();
+
+  JButton cancel = new JButton();
+
+  JPanel jPanel1 = new JPanel();
+
+  JLabel jLabel1 = new JLabel();
+
+  JPanel jPanel2 = new JPanel();
+
+  JPanel jPanel3 = new JPanel();
+
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  public void ok_actionPerformed(ActionEvent e)
+  {
+    if (lineart.isSelected())
+    {
+      value = "Lineart";
+    }
+    else
+    {
+      value = "Text";
+    }
+
+    if (!askAgain.isSelected())
+    {
+      jalview.bin.Cache.applicationProperties.remove("HTML_RENDERING");
+    }
+    else
+    {
+      jalview.bin.Cache.setProperty("HTML_RENDERING", value);
+    }
+
+    dialog.setVisible(false);
+  }
+
+  public void cancel_actionPerformed(ActionEvent e)
+  {
+    cancelled = true;
+    dialog.setVisible(false);
+  }
+
+  public String getValue()
+  {
+    return value;
+  }
+}
diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 91b23e4..6810fed 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -60,7 +60,7 @@ public class IdCanvas extends JPanel
 
   AnnotationPanel ap;
 
-  Font idfont;
+  private Font idfont;
 
   /**
    * Creates a new IdCanvas object.
@@ -119,7 +119,7 @@ public class IdCanvas extends JPanel
       gg.setColor(Color.black);
     }
 
-    if (av.rightAlignIds)
+    if (av.isRightAlignIds())
     {
       xPos = panelWidth
               - fm.stringWidth(s.getDisplayId(av.getShowJVSuffix())) - 4;
@@ -247,15 +247,15 @@ public class IdCanvas extends JPanel
   {
     if (av.seqNameItalics)
     {
-      idfont = new Font(av.getFont().getName(), Font.ITALIC, av.getFont()
-              .getSize());
+      setIdfont(new Font(av.getFont().getName(), Font.ITALIC, av.getFont()
+              .getSize()));
     }
     else
     {
-      idfont = av.getFont();
+      setIdfont(av.getFont());
     }
 
-    gg.setFont(idfont);
+    gg.setFont(getIdfont());
     fm = gg.getFontMetrics();
 
     if (av.antiAlias)
@@ -279,7 +279,7 @@ public class IdCanvas extends JPanel
 
       int annotationHeight = 0;
 
-      if (av.showAnnotation)
+      if (av.isShowAnnotation())
       {
         if (ap == null)
         {
@@ -316,13 +316,13 @@ public class IdCanvas extends JPanel
           }
           else
           {
-            gg.setFont(idfont);
+            gg.setFont(getIdfont());
           }
 
           drawIdString(gg, s, i, 0, ypos);
         }
 
-        if (labels != null && av.showAnnotation)
+        if (labels != null && av.isShowAnnotation())
         {
           gg.translate(0, ypos + (alheight * av.charHeight));
           labels.drawComponent(gg, getWidth());
@@ -383,7 +383,7 @@ public class IdCanvas extends JPanel
 
         String string = sequence.getDisplayId(av.getShowJVSuffix());
 
-        if (av.rightAlignIds)
+        if (av.isRightAlignIds())
         {
           xPos = panelWidth - fm.stringWidth(string) - 4;
         }
@@ -474,7 +474,7 @@ public class IdCanvas extends JPanel
     }
     else
     {
-      gg.setFont(idfont);
+      gg.setFont(getIdfont());
     }
   }
 
@@ -489,4 +489,14 @@ public class IdCanvas extends JPanel
     searchResults = list;
     repaint();
   }
+
+  public Font getIdfont()
+  {
+    return idfont;
+  }
+
+  public void setIdfont(Font idfont)
+  {
+    this.idfont = idfont;
+  }
 }
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 6b1109a..3486f72 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -52,7 +52,7 @@ import javax.swing.ToolTipManager;
 public class IdPanel extends JPanel implements MouseListener,
         MouseMotionListener, MouseWheelListener
 {
-  protected IdCanvas idCanvas;
+  private IdCanvas idCanvas;
 
   protected AlignViewport av;
 
@@ -81,11 +81,11 @@ public class IdPanel extends JPanel implements MouseListener,
   {
     this.av = av;
     alignPanel = parent;
-    idCanvas = new IdCanvas(av);
+    setIdCanvas(new IdCanvas(av));
     linkImageURL = getClass().getResource("/images/link.gif").toString();
     seqAnnotReport = new SequenceAnnotationReport(linkImageURL);
     setLayout(new BorderLayout());
-    add(idCanvas, BorderLayout.CENTER);
+    add(getIdCanvas(), BorderLayout.CENTER);
     addMouseListener(this);
     addMouseMotionListener(this);
     addMouseWheelListener(this);
@@ -102,7 +102,7 @@ public class IdPanel extends JPanel implements MouseListener,
   @Override
   public void mouseMoved(MouseEvent e)
   {
-    SeqPanel sp = alignPanel.seqPanel;
+    SeqPanel sp = alignPanel.getSeqPanel();
     int seq = Math.max(0, sp.findSeq(e));
     if (seq > -1 && seq < av.getAlignment().getHeight())
     {
@@ -128,7 +128,7 @@ public class IdPanel extends JPanel implements MouseListener,
   {
     mouseDragging = true;
 
-    int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
+    int seq = Math.max(0, alignPanel.getSeqPanel().findSeq(e));
 
     if (seq < lastid)
     {
@@ -202,7 +202,7 @@ public class IdPanel extends JPanel implements MouseListener,
       return;
     }
 
-    int seq = alignPanel.seqPanel.findSeq(e);
+    int seq = alignPanel.getSeqPanel().findSeq(e);
     String url = null;
     int i = 0;
     String id = av.getAlignment().getSequenceAt(seq).getName();
@@ -315,7 +315,7 @@ public class IdPanel extends JPanel implements MouseListener,
       return;
     }
 
-    int seq = alignPanel.seqPanel.findSeq(e);
+    int seq = alignPanel.getSeqPanel().findSeq(e);
 
     if (SwingUtilities.isRightMouseButton(e))
     {
@@ -443,7 +443,7 @@ public class IdPanel extends JPanel implements MouseListener,
    */
   public void highlightSearchResults(List<SequenceI> list)
   {
-    idCanvas.setHighlighted(list);
+    getIdCanvas().setHighlighted(list);
 
     if (list == null)
     {
@@ -459,6 +459,16 @@ public class IdPanel extends JPanel implements MouseListener,
     }
   }
 
+  public IdCanvas getIdCanvas()
+  {
+    return idCanvas;
+  }
+
+  public void setIdCanvas(IdCanvas idCanvas)
+  {
+    this.idCanvas = idCanvas;
+  }
+
   // this class allows scrolling off the bottom of the visible alignment
   class ScrollThread extends Thread
   {
diff --git a/src/jalview/gui/IdwidthAdjuster.java b/src/jalview/gui/IdwidthAdjuster.java
index 0c53c58..6c9c400 100755
--- a/src/jalview/gui/IdwidthAdjuster.java
+++ b/src/jalview/gui/IdwidthAdjuster.java
@@ -119,12 +119,12 @@ public class IdwidthAdjuster extends JPanel implements MouseListener,
   {
     active = true;
 
-    Dimension d = ap.idPanel.idCanvas.getPreferredSize();
+    Dimension d = ap.getIdPanel().getIdCanvas().getPreferredSize();
     int dif = evt.getX() - oldX;
 
     if (((d.width + dif) > 20) || (dif > 0))
     {
-      ap.idPanel.idCanvas.setPreferredSize(new Dimension(d.width + dif,
+      ap.getIdPanel().getIdCanvas().setPreferredSize(new Dimension(d.width + dif,
               d.height));
       ap.paintAlignment(true);
     }
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index b608b95..8ddd050 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1127,7 +1127,7 @@ public class Jalview2XML
       view.setShowBoxes(av.getShowBoxes());
       view.setShowColourText(av.getColourText());
       view.setShowFullId(av.getShowJVSuffix());
-      view.setRightAlignIds(av.rightAlignIds);
+      view.setRightAlignIds(av.isRightAlignIds());
       view.setShowSequenceFeatures(av.showSequenceFeatures);
       view.setShowText(av.getShowText());
       view.setShowUnconserved(av.getShowUnconserved());
@@ -1149,7 +1149,7 @@ public class Jalview2XML
       {
         jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
 
-        String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
+        String[] renderOrder = ap.getSeqPanel().seqCanvas.getFeatureRenderer().renderOrder;
 
         Vector settingsAdded = new Vector();
         Object gstyle = null;
@@ -1158,7 +1158,7 @@ public class Jalview2XML
         {
           for (int ro = 0; ro < renderOrder.length; ro++)
           {
-            gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer()
+            gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
                     .getFeatureStyle(renderOrder[ro]);
             Setting setting = new Setting();
             setting.setType(renderOrder[ro]);
@@ -1176,13 +1176,13 @@ public class Jalview2XML
             }
             else
             {
-              setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+              setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer()
                       .getColour(renderOrder[ro]).getRGB());
             }
 
             setting.setDisplay(av.featuresDisplayed
                     .containsKey(renderOrder[ro]));
-            float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer()
+            float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
                     .getOrder(renderOrder[ro]);
             if (rorder > -1)
             {
@@ -1194,7 +1194,7 @@ public class Jalview2XML
         }
 
         // Make sure we save none displayed feature settings
-        Iterator en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
+        Iterator en = ap.getSeqPanel().seqCanvas.getFeatureRenderer().featureColours
                 .keySet().iterator();
         while (en.hasNext())
         {
@@ -1206,11 +1206,11 @@ public class Jalview2XML
 
           Setting setting = new Setting();
           setting.setType(key);
-          setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+          setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer()
                   .getColour(key).getRGB());
 
           setting.setDisplay(false);
-          float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer()
+          float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
                   .getOrder(key);
           if (rorder > -1)
           {
@@ -1219,7 +1219,7 @@ public class Jalview2XML
           fs.addSetting(setting);
           settingsAdded.addElement(key);
         }
-        en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups
+        en = ap.getSeqPanel().seqCanvas.getFeatureRenderer().featureGroups
                 .keySet().iterator();
         Vector groupsAdded = new Vector();
         while (en.hasNext())
@@ -1231,7 +1231,7 @@ public class Jalview2XML
           }
           Group g = new Group();
           g.setName(grp);
-          g.setDisplay(((Boolean) ap.seqPanel.seqCanvas
+          g.setDisplay(((Boolean) ap.getSeqPanel().seqCanvas
                   .getFeatureRenderer().featureGroups.get(grp))
                   .booleanValue());
           fs.addGroup(g);
@@ -3472,7 +3472,7 @@ public class Jalview2XML
 
     af.viewport.setConservationSelected(view.getConservationSelected());
     af.viewport.setShowJVSuffix(view.getShowFullId());
-    af.viewport.rightAlignIds = view.getRightAlignIds();
+    af.viewport.setRightAlignIds(view.getRightAlignIds());
     af.viewport.setFont(new java.awt.Font(view.getFontName(), view
             .getFontStyle(), view.getFontSize()));
     af.alignPanel.fontChanged();
@@ -3633,24 +3633,24 @@ public class Jalview2XML
             gc.setColourByLabel(setting.getColourByLabel());
           }
           // and put in the feature colour table.
-          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
+          af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setColour(
                   setting.getType(), gc);
         }
         else
         {
-          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
+          af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setColour(
                   setting.getType(),
                   new java.awt.Color(setting.getColour()));
         }
         renderOrder[fs] = setting.getType();
         if (setting.hasOrder())
         {
-          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
+          af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setOrder(
                   setting.getType(), setting.getOrder());
         }
         else
         {
-          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
+          af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setOrder(
                   setting.getType(),
                   fs / jms.getFeatureSettings().getSettingCount());
         }
@@ -3660,9 +3660,9 @@ public class Jalview2XML
                   setting.getColour()));
         }
       }
-      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
+      af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
       Hashtable fgtable;
-      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
+      af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
       for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
       {
         Group grp = jms.getFeatureSettings().getGroup(gs);
diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index 9263cd9..9a58f51 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -422,7 +422,7 @@ public class Jalview2XML_V1
       {
         Setting setting = jms.getFeatureSettings().getSetting(fs);
 
-        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
+        af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setColour(
                 setting.getType(), new java.awt.Color(setting.getColour()));
 
         renderOrder[fs] = setting.getType();
@@ -433,7 +433,7 @@ public class Jalview2XML_V1
                   setting.getColour()));
         }
       }
-      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
+      af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
     }
 
     af.setMenusFromViewport(af.viewport);
diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index e8555f7..95e14b4 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -256,7 +256,7 @@ public class OverviewPanel extends JPanel implements Runnable
 
     if (av.showSequenceFeatures)
     {
-      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
+      fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer());
     }
 
     int alwidth = av.getAlignment().getWidth();
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 9976471..1a7235f 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1933,7 +1933,7 @@ public class PopupMenu extends JPopupMenu
                       true,
                       true,
                       false,
-                      (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
+                      (ap.getSeqPanel().seqCanvas.fr != null) ? ap.getSeqPanel().seqCanvas.fr.minmax
                               : null);
       contents.append("</p>");
     }
@@ -2650,7 +2650,7 @@ public class PopupMenu extends JPopupMenu
     System.arraycopy(features, 0, tfeatures, 0, rsize);
     features = tfeatures;
     seqs = rseqs;
-    if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+    if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
             features, true, ap))
     {
       ap.alignFrame.setShowSeqFeatures(true);
diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index ab0a0b8..c8a0ec7 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -107,7 +107,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     {
       public void internalFrameClosing(InternalFrameEvent evt)
       {
-        ap.idPanel.idCanvas.setHighlighted(null);
+        ap.getIdPanel().getIdCanvas().setHighlighted(null);
       }
     });
 
@@ -197,7 +197,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
         redundantSequences.add(originalSequences[i]);
       }
     }
-    ap.idPanel.idCanvas.setHighlighted(redundantSequences);
+    ap.getIdPanel().getIdCanvas().setHighlighted(redundantSequences);
   }
 
   /**
diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index f2c5154..568062b 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -327,7 +327,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
   {
     if (mouseDragging)
     {
-      ap.seqPanel.scrollCanvas(null);
+      ap.getSeqPanel().scrollCanvas(null);
     }
   }
 
@@ -335,7 +335,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
   {
     if (mouseDragging)
     {
-      ap.seqPanel.scrollCanvas(evt);
+      ap.getSeqPanel().scrollCanvas(evt);
     }
   }
 
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index d73ee70..54abcc2 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -573,7 +573,7 @@ public class SeqCanvas extends JComponent
 
       drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
 
-      if (av.showAnnotation)
+      if (av.isShowAnnotation())
       {
         g.translate(0, cHeight + ypos + 3);
         if (annotations == null)
@@ -598,7 +598,7 @@ public class SeqCanvas extends JComponent
 
   int getAnnotationHeight()
   {
-    if (!av.showAnnotation)
+    if (!av.isShowAnnotation())
     {
       return 0;
     }
@@ -627,7 +627,8 @@ public class SeqCanvas extends JComponent
    * @param offset
    *          DOCUMENT ME!
    */
-  void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,
+  public void drawPanel(Graphics g1, int startRes, int endRes,
+          int startSeq,
           int endSeq, int offset)
   {
     if (!av.hasHiddenColumns())
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index c10a4a9..de1ffdf 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -750,7 +750,7 @@ public class SeqPanel extends JPanel implements MouseListener,
               sequence.getDatasetSequence(),
               rpos = sequence.findPosition(res));
       seqARep.appendFeatures(tooltipText, rpos, features,
-              this.ap.seqPanel.seqCanvas.fr.minmax);
+              this.ap.getSeqPanel().seqCanvas.fr.minmax);
     }
     if (tooltipText.length() == 6) // <html></html>
     {
diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index 81b3bd3..cbd0d58 100755
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -300,7 +300,7 @@ public class SliderPanel extends GSliderPanel
       }
     }
 
-    ap.seqPanel.seqCanvas.repaint();
+    ap.getSeqPanel().seqCanvas.repaint();
   }
 
   /**
diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java
new file mode 100644
index 0000000..4643858
--- /dev/null
+++ b/src/jalview/io/HtmlSvgOutput.java
@@ -0,0 +1,264 @@
+package jalview.io;
+
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignViewport;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.AnnotationPanel;
+import jalview.gui.FeatureRenderer;
+import jalview.gui.HTMLOptions;
+import jalview.math.AlignmentDimension;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.print.Printable;
+import java.awt.print.PrinterException;
+import java.io.File;
+import java.io.FileOutputStream;
+
+import org.jfree.graphics2d.svg.SVGGraphics2D;
+import org.jfree.graphics2d.svg.SVGHints;
+
+public class HtmlSvgOutput
+{
+  AlignViewport av;
+
+  FeatureRenderer fr;
+  AlignmentPanel ap;
+
+  AnnotationPanel annotationPanel;
+
+  public HtmlSvgOutput(AlignmentPanel ap)
+  {
+
+      this.av = ap.av;
+      this.ap = ap;
+      this.annotationPanel = ap.getAnnotationPanel();
+    generateHtmlSvgOutput();
+  }
+
+  public void generateHtmlSvgOutput()
+  {
+    File file = null;
+    try
+    {
+      JalviewFileChooser chooser = getHTMLChooser();
+      chooser.setFileView(new jalview.io.JalviewFileView());
+      chooser.setDialogTitle(ap.alignFrame.getTitle());
+      chooser.setToolTipText(MessageManager.getString("action.save"));
+      int value = chooser.showSaveDialog(ap.alignFrame);
+
+      if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+      {
+        jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+                .getSelectedFile().getParent());
+        file = chooser.getSelectedFile();
+      }
+
+      AlignmentDimension aDimension = ap.getAlignmentDimension();
+      SVGGraphics2D g1 = new SVGGraphics2D(aDimension.getWidth(),
+              aDimension.getHeight());
+      SVGGraphics2D g2 = new SVGGraphics2D(aDimension.getWidth(),
+              aDimension.getHeight());
+
+      String renderStyle = jalview.bin.Cache.getDefault("HTML_RENDERING",
+              "Prompt each time");
+
+      // If we need to prompt, and if the GUI is visible then
+      // Prompt for rendering style
+      if (renderStyle.equalsIgnoreCase("Prompt each time")
+              && !(System.getProperty("java.awt.headless") != null && System
+                      .getProperty("java.awt.headless").equals("true")))
+      {
+        HTMLOptions svgOption = new HTMLOptions();
+        renderStyle = svgOption.getValue();
+
+        if (renderStyle == null || svgOption.cancelled)
+        {
+          return;
+        }
+      }
+
+      if (renderStyle.equalsIgnoreCase("lineart"))
+      {
+        g1.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
+                SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
+        g2.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
+                SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
+      }
+      printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0, g1,
+              g2);
+      FileOutputStream out = new FileOutputStream(file);
+
+      String titleSvgData = g1.getSVGDocument();
+      String alignSvgData = g2.getSVGDocument();
+      String htmlData = getHtml(titleSvgData, alignSvgData);
+
+      out.write(htmlData.getBytes());
+      out.flush();
+      out.close();
+
+      jalview.util.BrowserLauncher.openURL("file:///" + file);
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+  }
+  
+  static JalviewFileChooser getHTMLChooser()
+  {
+    return new jalview.io.JalviewFileChooser(
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+            { "html" }, new String[]
+            { "Hypertext Markup Language" }, "Hypertext Markup Language");
+  }
+
+  public int printUnwrapped(int pwidth, int pheight, int pi, Graphics... pg)
+          throws PrinterException
+  {
+    int idWidth = ap.getVisibleIdWidth(false);
+    FontMetrics fm = ap.getFontMetrics(av.getFont());
+    int scaleHeight = av.getCharHeight() + fm.getDescent();
+
+    pg[0].setColor(Color.white);
+    pg[0].fillRect(0, 0, pwidth, pheight);
+    pg[0].setFont(av.getFont());
+
+    // //////////////////////////////////
+    // / How many sequences and residues can we fit on a printable page?
+    int totalRes = (pwidth - idWidth) / av.getCharWidth();
+    int totalSeq = (pheight - scaleHeight) / av.getCharHeight() - 1;
+    int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
+
+    // ///////////////////////////
+    // / Only print these sequences and residues on this page
+    int startRes;
+
+    // ///////////////////////////
+    // / Only print these sequences and residues on this page
+    int endRes;
+
+    // ///////////////////////////
+    // / Only print these sequences and residues on this page
+    int startSeq;
+
+    // ///////////////////////////
+    // / Only print these sequences and residues on this page
+    int endSeq;
+    startRes = (pi % pagesWide) * totalRes;
+    endRes = (startRes + totalRes) - 1;
+
+    if (endRes > (av.getAlignment().getWidth() - 1))
+    {
+      endRes = av.getAlignment().getWidth() - 1;
+    }
+    startSeq = (pi / pagesWide) * totalSeq;
+    endSeq = startSeq + totalSeq;
+    if (endSeq > av.getAlignment().getHeight())
+    {
+      endSeq = av.getAlignment().getHeight();
+    }
+    int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1)
+            * pheight;
+    if (av.isShowAnnotation())
+    {
+      pagesHigh += ap.getAnnotationPanel().adjustPanelHeight() + 3;
+    }
+    pagesHigh /= pheight;
+    if (pi >= (pagesWide * pagesHigh))
+    {
+      return Printable.NO_SUCH_PAGE;
+    }
+
+    // draw Scale
+    pg[1].translate(0, 0);
+    ap.getScalePanel().drawScale(pg[1], startRes, endRes, pwidth - idWidth,
+            scaleHeight);
+    pg[1].translate(-idWidth, scaleHeight);
+
+    // //////////////
+    // Draw the ids
+    Color currentColor = null;
+    Color currentTextColor = null;
+    pg[0].translate(0, scaleHeight);
+    pg[0].setFont(ap.getIdPanel().getIdCanvas().getIdfont());
+    SequenceI seq;
+    for (int i = startSeq; i < endSeq; i++)
+    {
+      seq = av.getAlignment().getSequenceAt(i);
+      if ((av.getSelectionGroup() != null)
+              && av.getSelectionGroup().getSequences(null).contains(seq))
+      {
+        currentColor = Color.gray;
+        currentTextColor = Color.black;
+      }
+      else
+      {
+        currentColor = av.getSequenceColour(seq);
+        currentTextColor = Color.black;
+      }
+      pg[0].setColor(currentColor);
+      pg[0].fillRect(0, (i - startSeq) * av.getCharHeight(), idWidth,
+              av.getCharHeight());
+      pg[0].setColor(currentTextColor);
+      int xPos = 0;
+      if (av.isRightAlignIds())
+      {
+        fm = pg[0].getFontMetrics();
+        xPos = idWidth
+                - fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix()))
+                - 4;
+      }
+      pg[0].drawString(
+              seq.getDisplayId(av.getShowJVSuffix()),
+              xPos,
+              (((i - startSeq) * av.getCharHeight()) + av.getCharHeight())
+                      - (av.getCharHeight() / 5));
+    }
+    pg[0].setFont(av.getFont());
+    pg[0].translate(idWidth, 0);
+
+    // draw main sequence panel
+    pg[1].translate(idWidth, 0);
+    ap.getSeqPanel().seqCanvas.drawPanel(pg[1], startRes, endRes, startSeq,
+            endSeq, 0);
+    if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight()))
+    {
+      // draw annotation label - need to offset for current scroll position
+      int offset = -ap.getAlabels().getScrollOffset();
+      pg[0].translate(0, offset);
+      pg[0].translate(-idWidth - 3,
+              (endSeq - startSeq) * av.getCharHeight() + 3);
+      ap.getAlabels().drawComponent(pg[0], idWidth);
+      pg[0].translate(idWidth + 3, 0);
+      pg[0].translate(0, -offset);
+
+      // draw annotation - need to offset for current scroll position
+      pg[1].translate(0, offset);
+      pg[1].translate(-idWidth - 3,
+              (endSeq - startSeq) * av.getCharHeight() + 3);
+      pg[1].translate(idWidth + 3, 0);
+      ap.getAnnotationPanel().renderer.drawComponent(
+              ap.getAnnotationPanel(), av, pg[1], -1, startRes, endRes + 1);
+      pg[1].translate(0, -offset);
+    }
+
+    return Printable.PAGE_EXISTS;
+  }
+  
+  private String getHtml(String titleSvg, String alignmentSvg)
+  {
+    StringBuilder htmlSvg = new StringBuilder();
+    htmlSvg.append("<html><style type=\"text/css\">" + "div.title {"
+            + "height: 100%;" + "width: 9%;" + "float: left;" + "}"
+            + "div.align {" + "height: 100%;" + "width: 91%;"
+            + "overflow: scroll;" + "float: right;" + "}" + "</style>"
+            + "<div style=\"width:100%; height:100%; overflow: hidden\">"
+            + "<div class=\"title\">");
+    htmlSvg.append(titleSvg);
+    htmlSvg.append("</div><div class=\"align\">").append(alignmentSvg);
+    htmlSvg.append("</div>");
+    return htmlSvg.toString();
+  }
+}
diff --git a/src/jalview/math/AlignmentDimension.java b/src/jalview/math/AlignmentDimension.java
new file mode 100644
index 0000000..ea3abf4
--- /dev/null
+++ b/src/jalview/math/AlignmentDimension.java
@@ -0,0 +1,35 @@
+package jalview.math;
+
+public class AlignmentDimension
+{
+  private int width;
+
+  private int height;
+
+  public AlignmentDimension(int width, int height)
+  {
+    this.width = width;
+    this.height = height;
+  }
+
+  public int getWidth()
+  {
+    return width;
+  }
+
+  public void setWidth(int width)
+  {
+    this.width = width;
+  }
+
+  public int getHeight()
+  {
+    return height;
+  }
+
+  public void setHeight(int height)
+  {
+    this.height = height;
+  }
+
+}