X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=7132ff0662cad5b167d6b22d8abec5a8ed1f1ff7;hb=49ff786d8e7d016cac6895539e6fb0eac8aae95c;hp=bcfb0884c786eb7ac035f18f3d4ac1814570ec3b;hpb=c564d188c1a8106d866651eba5c4cf60fbc0c232;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index bcfb088..7132ff0 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,38 +1,59 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
-import java.beans.*;
-import java.io.*;
-import java.util.Hashtable;
-import java.util.Vector;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.print.*;
-import javax.swing.*;
-
+import jalview.analysis.AnnotationSorter;
+import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+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;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.print.PageFormat;
+import java.awt.print.Printable;
+import java.awt.print.PrinterException;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.PrintWriter;
+
+import javax.swing.SwingUtilities;
 
 /**
  * DOCUMENT ME!
@@ -47,20 +68,21 @@ 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;
@@ -73,36 +95,32 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * Creates a new AlignmentPanel object.
    * 
    * @param af
-   *          DOCUMENT ME!
    * @param av
-   *          DOCUMENT ME!
    */
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
     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);
 
-    setAnnotationVisible(av.getShowAnnotation());
-
     hscroll.addAdjustmentListener(this);
     vscroll.addAdjustmentListener(this);
 
@@ -120,9 +138,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
     });
     fontChanged();
     adjustAnnotationHeight();
-
+    updateLayout();
   }
 
+  @Override
+  public AlignViewportI getAlignViewport()
+  {
+    return av;
+  }
   public void alignmentChanged()
   {
     av.alignmentChanged(this);
@@ -142,18 +165,20 @@ public class AlignmentPanel extends GAlignmentPanel implements
     // to prevent drawing old image
     FontMetrics fm = getFontMetrics(av.getFont());
 
-    scalePanelHolder.setPreferredSize(new Dimension(10, av.charHeight
+    scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight()
             + fm.getDescent()));
-    idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av.charHeight
+    idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av
+            .getCharHeight()
             + 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)
@@ -173,15 +198,41 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public Dimension calculateIdWidth()
   {
+    // calculate sensible default width when no preference is available
+    Dimension r = null;
+    if (av.getIdWidth() < 0)
+    {
+      int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
+      int maxwidth = Math.max(20, Math.min(afwidth - 200, 2 * afwidth / 3));
+      r = calculateIdWidth(maxwidth);
+      av.setIdWidth(r.width);
+    }
+    else
+    {
+      r = new Dimension();
+      r.width = av.getIdWidth();
+      r.height = 0;
+    }
+    return r;
+  }
+
+  /**
+   * Calculate the width of the alignment labels based on the displayed names
+   * and any bounds on label width set in preferences.
+   * 
+   * @param maxwidth
+   *          -1 or maximum width allowed for IdWidth
+   * @return Dimension giving the maximum width of the alignment label panel
+   *         that should be used.
+   */
+  public Dimension calculateIdWidth(int maxwidth)
+  {
     Container c = new Container();
 
     FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(),
             Font.ITALIC, av.font.getSize()));
 
     AlignmentI al = av.getAlignment();
-    int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
-    int maxwidth = Math.max(20,
-            Math.min(afwidth - 200, (int) 2 * afwidth / 3));
     int i = 0;
     int idWidth = 0;
     String id;
@@ -205,7 +256,7 @@ 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)
       {
@@ -220,7 +271,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
     }
 
-    return new Dimension(Math.min(maxwidth, idWidth), 12);
+    return new Dimension(maxwidth < 0 ? idWidth : Math.min(maxwidth,
+            idWidth), 12);
   }
 
   /**
@@ -230,7 +282,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   public void highlightSearchResults(SearchResults results)
   {
     scrollToPosition(results);
-    seqPanel.seqCanvas.highlightSearchResults(results);
+    getSeqPanel().seqCanvas.highlightSearchResults(results);
   }
 
   /**
@@ -262,16 +314,16 @@ public class AlignmentPanel extends GAlignmentPanel implements
     // do we need to scroll the panel?
     // TODO: tons of nullpointereexceptions raised here.
     if (results != null && results.getSize() > 0 && av != null
-            && av.alignment != null)
+            && av.getAlignment() != null)
     {
-      int seqIndex = av.alignment.findIndex(results);
+      int seqIndex = av.getAlignment().findIndex(results);
       if (seqIndex == -1)
       {
         return false;
       }
-      SequenceI seq = av.alignment.getSequenceAt(seqIndex);
-      
-      int[] r=results.getResults(seq, 0, av.alignment.getWidth());
+      SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
+
+      int[] r = results.getResults(seq, 0, av.getAlignment().getWidth());
       if (r == null)
       {
         return false;
@@ -288,20 +340,20 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         return false;
       }
-      if (av.hasHiddenColumns)
+      if (av.hasHiddenColumns())
       {
         start = av.getColumnSelection().findColumnPosition(start);
         end = av.getColumnSelection().findColumnPosition(end);
-        if (start==end)
+        if (start == end)
         {
-          if (!av.colSel.isVisible(r[0]))
+          if (!av.getColumnSelection().isVisible(r[0]))
           {
             // don't scroll - position isn't visible
             return false;
           }
         }
       }
-      if (!av.wrapAlignment)
+      if (!av.getWrapAlignment())
       {
         if ((startv = av.getStartRes()) >= start)
         {
@@ -335,8 +387,8 @@ 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));
@@ -368,12 +420,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   /**
    * 
-   * @param b Hide or show annotation panel
-   *          
+   * @param b
+   *          Hide or show annotation panel
+   * 
    */
   public void setAnnotationVisible(boolean b)
   {
-    if (!av.wrapAlignment)
+    if (!av.getWrapAlignment())
     {
       annotationSpaceFillerHolder.setVisible(b);
       annotationScroller.setVisible(b);
@@ -382,8 +435,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * automatically adjust annotation panel height for new annotation
-   * whilst ensuring the alignment is still visible.
+   * automatically adjust annotation panel height for new annotation whilst
+   * ensuring the alignment is still visible.
    */
   public void adjustAnnotationHeight()
   {
@@ -397,28 +450,48 @@ public class AlignmentPanel extends GAlignmentPanel implements
     addNotify();
     paintAlignment(true);
   }
+
   /**
    * calculate the annotation dimensions and refresh slider values accordingly.
-   * need to do repaints/notifys afterwards. 
+   * need to do repaints/notifys afterwards.
    */
-  protected void validateAnnotationDimensions(boolean adjustPanelHeight) {
-    int height = annotationPanel.adjustPanelHeight();
-    
-    if (hscroll.isVisible())
-    {
-      height += hscroll.getPreferredSize().height;
-    }
-    if (height > alignFrame.getHeight() / 2)
-    {
-      height = alignFrame.getHeight() / 2;
+  protected void validateAnnotationDimensions(boolean adjustPanelHeight)
+  {
+    int height = getAnnotationPanel().adjustPanelHeight();
+
+    int theight = av.getCharHeight()
+            * (av.getAlignment().getHeight() + (!av.hasHiddenRows() ? 0
+                    : av.getAlignment().getHiddenSequences().getSize()));
+    float sscaling = (float) (theight / (1.0 * theight + height));
+    float ascaling = (float) (height * 1.0 / alignFrame.getHeight());
+    int rheight = alignFrame.getHeight() - height - av.getCharHeight();
+    if (adjustPanelHeight)
+    {
+      // NOTE: this logic is different in the applet. Need a better algorithm to
+      // define behaviour
+      // try and set height according to alignment
+      if (ascaling > 0 && sscaling < 0.5)
+      {
+        // if the alignment is too big then
+        // default is 0.5 split
+        height = alignFrame.getHeight() / 2;
+      }
+      else
+      {
+        // if space for more than one sequence row left when annotation is fully
+        // displayed then set height to annotation height
+        // otherwise, leave at least two lines of sequence shown.
+        height = (rheight > av.getCharHeight()) ? height
+                : (-av.getCharHeight() * 3 + (int) (alignFrame.getHeight() * (1 - sscaling)));
+      }
     }
-    if (!adjustPanelHeight)
+    else
     {
       // maintain same window layout whilst updating sliders
-      height=annotationScroller.getSize().height;
+      height = annotationScroller.getSize().height;
     }
     hscroll.addNotify();
-    
+
     annotationScroller.setPreferredSize(new Dimension(annotationScroller
             .getWidth(), height));
 
@@ -429,13 +502,16 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * DOCUMENT ME!
+   * update alignment layout for viewport settings
    * 
    * @param wrap
    *          DOCUMENT ME!
    */
-  public void setWrapAlignment(boolean wrap)
+  public void updateLayout()
   {
+    fontChanged();
+    setAnnotationVisible(av.isShowAnnotation());
+    boolean wrap = av.getWrapAlignment();
     av.startSeq = 0;
     scalePanelHolder.setVisible(!wrap);
     hscroll.setVisible(!wrap);
@@ -446,7 +522,7 @@ 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);
@@ -525,30 +601,32 @@ public class AlignmentPanel extends GAlignmentPanel implements
   /**
    * Adjust row/column scrollers to show a visible position in the alignment.
    * 
-   * @param x visible column to scroll to
-   *          DOCUMENT ME!
-   * @param y visible row to scroll to
-   *          
+   * @param x
+   *          visible column to scroll to DOCUMENT ME!
+   * @param y
+   *          visible row to scroll to
+   * 
    */
   public void setScrollValues(int x, int y)
   {
     // System.err.println("Scroll to "+x+","+y);
-    if (av == null || av.alignment == null)
+    if (av == null || av.getAlignment() == null)
     {
       return;
     }
-    int width = av.alignment.getWidth();
-    int height = av.alignment.getHeight();
+    int width = av.getAlignment().getWidth();
+    int height = av.getAlignment().getHeight();
 
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       width = av.getColumnSelection().findColumnPosition(width);
     }
 
-    av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1);
+    av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+            .getCharWidth())) - 1);
 
-    hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
-    vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
+    hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
+    vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
 
     if (hextent > width)
     {
@@ -592,7 +670,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
-
     int oldX = av.getStartRes();
     int oldY = av.getStartSeq();
 
@@ -600,7 +677,7 @@ 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)
@@ -611,8 +688,8 @@ 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);
         }
@@ -634,7 +711,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         av.setStartSeq(offy);
         av.setEndSeq(offy
-                + (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
+                + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight()));
       }
     }
 
@@ -665,20 +742,29 @@ 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())
+        if (av.isShowAnnotation() && scrollX != 0)
         {
-          annotationPanel.fastPaint(scrollX);
+          getAnnotationPanel().fastPaint(scrollX);
         }
       }
     }
   }
 
+  /**
+   * Repaint the alignment including the annotations and overview panels (if
+   * shown).
+   */
   public void paintAlignment(boolean updateOverview)
   {
+    final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
+            av.isShowAutocalculatedAbove());
+    sorter.sort(getAlignment()
+            .getAlignmentAnnotation(),
+            av.getSortAnnotationsBy());
     repaint();
 
     if (updateOverview)
@@ -702,27 +788,27 @@ 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();
 
     if (av.getWrapAlignment())
     {
-      int maxwidth = av.alignment.getWidth();
+      int maxwidth = av.getAlignment().getWidth();
 
-      if (av.hasHiddenColumns)
+      if (av.hasHiddenColumns())
       {
         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);
@@ -788,9 +874,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
   public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
           throws PrinterException
   {
-    int idWidth = getVisibleIdWidth();
+    int idWidth = getVisibleIdWidth(false);
     FontMetrics fm = getFontMetrics(av.getFont());
-    int scaleHeight = av.charHeight + fm.getDescent();
+    int scaleHeight = av.getCharHeight() + fm.getDescent();
 
     pg.setColor(Color.white);
     pg.fillRect(0, 0, pwidth, pheight);
@@ -800,7 +886,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     // / How many sequences and residues can we fit on a printable page?
     int totalRes = (pwidth - idWidth) / av.getCharWidth();
 
-    int totalSeq = (int) ((pheight - scaleHeight) / av.getCharHeight()) - 1;
+    int totalSeq = (pheight - scaleHeight) / av.getCharHeight() - 1;
 
     int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
 
@@ -835,11 +921,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
       endSeq = av.getAlignment().getHeight();
     }
 
-    int pagesHigh = ((av.alignment.getHeight() / totalSeq) + 1) * pheight;
+    int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1)
+            * pheight;
 
-    if (av.showAnnotation)
+    if (av.isShowAnnotation())
     {
-      pagesHigh += annotationPanel.adjustPanelHeight() + 3;
+      pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
     }
 
     pagesHigh /= pheight;
@@ -851,7 +938,7 @@ 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);
 
@@ -860,7 +947,7 @@ 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++)
@@ -879,13 +966,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
 
       pg.setColor(currentColor);
-      pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
+      pg.fillRect(0, (i - startSeq) * av.getCharHeight(), idWidth,
               av.getCharHeight());
 
       pg.setColor(currentTextColor);
 
       int xPos = 0;
-      if (av.rightAlignIds)
+      if (av.isRightAlignIds())
       {
         fm = pg.getFontMetrics();
         xPos = idWidth
@@ -896,7 +983,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       pg.drawString(
               seq.getDisplayId(av.getShowJVSuffix()),
               xPos,
-              (((i - startSeq) * av.charHeight) + av.getCharHeight())
+              (((i - startSeq) * av.getCharHeight()) + av.getCharHeight())
                       - (av.getCharHeight() / 5));
     }
 
@@ -904,14 +991,20 @@ 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.alignment.getHeight()))
+    if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight()))
     {
-      pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
-      alabels.drawComponent((Graphics2D) pg, idWidth);
+      // draw annotation - need to offset for current scroll position
+      int offset = -getAlabels().getScrollOffset();
+      pg.translate(0, offset);
+      pg.translate(-idWidth - 3, (endSeq - startSeq) * av.getCharHeight()
+              + 3);
+      getAlabels().drawComponent(pg, idWidth);
       pg.translate(idWidth + 3, 0);
-      annotationPanel.renderer.drawComponent(annotationPanel, av, (Graphics2D) pg, -1, startRes, endRes + 1);
+      getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
+              pg, -1, startRes, endRes + 1);
+      pg.translate(0, -offset);
     }
 
     return Printable.PAGE_EXISTS;
@@ -937,33 +1030,32 @@ public class AlignmentPanel extends GAlignmentPanel implements
   public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
           int pi) throws PrinterException
   {
-
     int annotationHeight = 0;
     AnnotationLabels labels = null;
-    if (av.showAnnotation)
+    if (av.isShowAnnotation())
     {
-      annotationHeight = annotationPanel.adjustPanelHeight();
+      annotationHeight = getAnnotationPanel().adjustPanelHeight();
       labels = new AnnotationLabels(av);
     }
 
-    int hgap = av.charHeight;
-    if (av.scaleAboveWrapped)
+    int hgap = av.getCharHeight();
+    if (av.getScaleAboveWrapped())
     {
-      hgap += av.charHeight;
+      hgap += av.getCharHeight();
     }
 
-    int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+    int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
             + annotationHeight;
 
-    int idWidth = getVisibleIdWidth();
+    int idWidth = getVisibleIdWidth(false);
 
-    int maxwidth = av.alignment.getWidth();
-    if (av.hasHiddenColumns)
+    int maxwidth = av.getAlignment().getWidth();
+    if (av.hasHiddenColumns())
     {
       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);
@@ -984,30 +1076,31 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     do
     {
-      for (int i = 0; i < av.alignment.getHeight(); i++)
+      for (int i = 0; i < av.getAlignment().getHeight(); i++)
       {
-        pg.setFont(idPanel.idCanvas.idfont);
-        SequenceI s = av.alignment.getSequenceAt(i);
+        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;
         }
         pg.drawString(string, xPos,
-                ((i * av.charHeight) + ypos + av.charHeight)
-                        - (av.charHeight / 5));
+                ((i * av.getCharHeight()) + ypos + av.getCharHeight())
+                        - (av.getCharHeight() / 5));
       }
       if (labels != null)
       {
         pg.translate(-3, ypos
-                + (av.getAlignment().getHeight() * av.charHeight));
+ + (av.getAlignment().getHeight() * av.getCharHeight()));
 
         pg.setFont(av.getFont());
         labels.drawComponent(pg, idWidth);
         pg.translate(+3, -ypos
-                - (av.getAlignment().getHeight() * av.charHeight));
+                        - (av.getAlignment().getHeight() * av
+                                .getCharHeight()));
       }
 
       ypos += cHeight;
@@ -1015,7 +1108,7 @@ 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)
@@ -1029,90 +1122,156 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
   }
 
-  int getVisibleIdWidth()
+  /**
+   * get current sequence ID panel width, or nominal value if panel were to be
+   * displayed using default settings
+   * 
+   * @return
+   */
+  public int getVisibleIdWidth()
   {
-    return idPanel.getWidth() > 0 ? idPanel.getWidth()
-            : calculateIdWidth().width + 4;
+    return getVisibleIdWidth(true);
   }
 
-  void makeAlignmentImage(int type, File file)
+  /**
+   * get current sequence ID panel width, or nominal value if panel were to be
+   * displayed using default settings
+   * 
+   * @param onscreen
+   *          indicate if the Id width for onscreen or offscreen display should
+   *          be returned
+   * @return
+   */
+  public int getVisibleIdWidth(boolean onscreen)
   {
-    int maxwidth = av.alignment.getWidth();
-    if (av.hasHiddenColumns)
+    // see if rendering offscreen - check preferences and calc width accordingly
+    if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
     {
-      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
+      return calculateIdWidth(-1).width + 4;
     }
+    Integer idwidth = null;
+    if (onscreen
+            || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
+    {
+      return (getIdPanel().getWidth() > 0 ? getIdPanel().getWidth()
+              : calculateIdWidth().width + 4);
+    }
+    return idwidth.intValue() + 4;
+  }
 
-    int height = ((av.alignment.getHeight() + 1) * av.charHeight)
-            + scalePanel.getHeight();
-    int width = getVisibleIdWidth() + (maxwidth * av.charWidth);
-
-    if (av.getWrapAlignment())
+  void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
+  {
+    long progress = System.currentTimeMillis();
+    headless = (System.getProperty("java.awt.headless") != null && System
+            .getProperty("java.awt.headless").equals("true"));
+    if (alignFrame != null && !headless)
+    {
+      alignFrame.setProgressBar(MessageManager.formatMessage(
+              "status.saving_file", new Object[]
+              { type.getLabel() }), progress);
+    }
+    try
     {
-      height = getWrappedHeight();
-      if (System.getProperty("java.awt.headless") != null
-              && System.getProperty("java.awt.headless").equals("true"))
+      AlignmentDimension aDimension = getAlignmentDimension();
+      try
       {
-        // TODO: JAL-244
-        width = alignFrame.getWidth() - vscroll.getPreferredSize().width
-                - alignFrame.getInsets().left
-                - alignFrame.getInsets().right;
+        jalview.util.ImageMaker im;
+        final String imageAction, imageTitle;
+        if (type == jalview.util.ImageMaker.TYPE.PNG)
+        {
+          imageAction = "Create PNG image from alignment";
+          imageTitle = null;
+        }
+        else if (type == jalview.util.ImageMaker.TYPE.EPS)
+        {
+          imageAction = "Create EPS file from alignment";
+          imageTitle = alignFrame.getTitle();
+        }
+        else
+        {
+          imageAction = "Create SVG file from alignment";
+          imageTitle = alignFrame.getTitle();
+        }
+
+        im = new jalview.util.ImageMaker(this, type, imageAction,
+                aDimension.getWidth(), aDimension.getHeight(), file,
+                imageTitle);
+        if (av.getWrapAlignment())
+        {
+          if (im.getGraphics() != null)
+          {
+            printWrappedAlignment(im.getGraphics(), aDimension.getWidth(),
+                    aDimension.getHeight(), 0);
+            im.writeImage();
+          }
+        }
+        else
+        {
+          if (im.getGraphics() != null)
+          {
+            printUnwrapped(im.getGraphics(), aDimension.getWidth(),
+                    aDimension.getHeight(), 0);
+            im.writeImage();
+          }
+        }
+      } catch (OutOfMemoryError err)
+      {
+        // Be noisy here.
+        System.out.println("########################\n" + "OUT OF MEMORY "
+                + file + "\n" + "########################");
+        new OOMWarning("Creating Image for " + file, err);
+        // System.out.println("Create IMAGE: " + err);
+      } catch (Exception ex)
+      {
+        ex.printStackTrace();
       }
-      else
+    } finally
+    {
+      if (alignFrame != null && !headless)
       {
-        width = seqPanel.getWidth() + getVisibleIdWidth();
+        alignFrame.setProgressBar(MessageManager.getString("status.export_complete"), progress);
       }
-
     }
-    else if (av.getShowAnnotation())
+  }
+
+  public AlignmentDimension getAlignmentDimension()
+  {
+    int maxwidth = av.getAlignment().getWidth();
+    if (av.hasHiddenColumns())
     {
-      height += annotationPanel.adjustPanelHeight() + 3;
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
     }
 
-    try
-    {
+    int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
+            + getScalePanel().getHeight();
+    int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
 
-      jalview.util.ImageMaker im;
-      if (type == jalview.util.ImageMaker.PNG)
+    if (av.getWrapAlignment())
+    {
+      height = getWrappedHeight();
+      if (headless)
       {
-        im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
-                "Create PNG image from alignment", width, height, file,
-                null);
+        // 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
       {
-        im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
-                "Create EPS file from alignment", width, height, file,
-                alignFrame.getTitle());
+        width = getSeqPanel().getWidth() + getVisibleIdWidth(false);
       }
 
-      if (av.getWrapAlignment())
-      {
-        if (im.getGraphics() != null)
-        {
-          printWrappedAlignment(im.getGraphics(), width, height, 0);
-          im.writeImage();
-        }
-      }
-      else
-      {
-        if (im.getGraphics() != null)
-        {
-          printUnwrapped(im.getGraphics(), width, height, 0);
-          im.writeImage();
-        }
-      }
-    } catch (OutOfMemoryError err)
-    {
-      // Be noisy here.
-      System.out.println("########################\n" + "OUT OF MEMORY "
-              + file + "\n" + "########################");
-      new OOMWarning("Creating Image for " + file, err);
-      // System.out.println("Create IMAGE: " + err);
-    } catch (Exception ex)
+    }
+    else if (av.isShowAnnotation())
     {
-      ex.printStackTrace();
+      height += getAnnotationPanel().adjustPanelHeight() + 3;
     }
+    return new AlignmentDimension(width, height);
+
   }
 
   /**
@@ -1120,7 +1279,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public void makeEPS(File epsFile)
   {
-    makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
+    makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile);
   }
 
   /**
@@ -1128,16 +1287,20 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public void makePNG(File pngFile)
   {
-    makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
+    makeAlignmentImage(jalview.util.ImageMaker.TYPE.PNG, pngFile);
   }
 
+  public void makeSVG(File svgFile)
+  {
+    makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
+  }
   public void makePNGImageMap(File imgMapFile, String imageName)
   {
     // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
     // ////////////////////////////////////////////
-    int idWidth = getVisibleIdWidth();
+    int idWidth = getVisibleIdWidth(false);
     FontMetrics fm = getFontMetrics(av.getFont());
-    int scaleHeight = av.charHeight + fm.getDescent();
+    int scaleHeight = av.getCharHeight() + fm.getDescent();
 
     // Gen image map
     // ////////////////////////////////
@@ -1145,8 +1308,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       try
       {
-        int s, sSize = av.alignment.getHeight(), res, alwidth = av.alignment
-                .getWidth(), g, gSize, f, fSize, sy;
+        int s, sSize = av.getAlignment().getHeight(), res, alwidth = av
+                .getAlignment().getWidth(), g, gSize, f, fSize, sy;
         StringBuffer text = new StringBuffer();
         PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
         out.println(jalview.io.HTMLOutput.getImageMapHTML());
@@ -1156,33 +1319,33 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
         for (s = 0; s < sSize; s++)
         {
-          sy = s * av.charHeight + scaleHeight;
+          sy = s * av.getCharHeight() + scaleHeight;
 
-          SequenceI seq = av.alignment.getSequenceAt(s);
+          SequenceI seq = av.getAlignment().getSequenceAt(s);
           SequenceFeature[] features = seq.getDatasetSequence()
                   .getSequenceFeatures();
-          SequenceGroup[] groups = av.alignment.findAllGroups(seq);
+          SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
           for (res = 0; res < alwidth; res++)
           {
             text = new StringBuffer();
-            Object obj = null;
-            if (av.alignment.isNucleotide())
+            String triplet = null;
+            if (av.getAlignment().isNucleotide())
             {
-              obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)
+              triplet = ResidueProperties.nucleotideName.get(seq
+                      .getCharAt(res)
                       + "");
             }
             else
             {
-              obj = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
+              triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
                       + "");
             }
 
-            if (obj == null)
+            if (triplet == null)
             {
               continue;
             }
 
-            String triplet = obj.toString();
             int alIndex = seq.findPosition(res);
             gSize = groups.length;
             for (g = 0; g < gSize; g++)
@@ -1190,9 +1353,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
               if (text.length() < 1)
               {
                 text.append("<area shape=\"rect\" coords=\""
-                        + (idWidth + res * av.charWidth) + "," + sy + ","
-                        + (idWidth + (res + 1) * av.charWidth) + ","
-                        + (av.charHeight + sy) + "\""
+                        + (idWidth + res * av.getCharWidth()) + "," + sy
+                        + "," + (idWidth + (res + 1) * av.getCharWidth())
+                        + ","
+                        + (av.getCharHeight() + sy) + "\""
                         + " onMouseOver=\"toolTip('" + alIndex + " "
                         + triplet);
               }
@@ -1209,9 +1373,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
               if (text.length() < 1)
               {
                 text.append("<area shape=\"rect\" coords=\""
-                        + (idWidth + res * av.charWidth) + "," + sy + ","
-                        + (idWidth + (res + 1) * av.charWidth) + ","
-                        + (av.charHeight + sy) + "\""
+                        + (idWidth + res * av.getCharWidth()) + "," + sy
+                        + "," + (idWidth + (res + 1) * av.getCharWidth())
+                        + ","
+                        + (av.getCharHeight() + sy) + "\""
                         + " onMouseOver=\"toolTip('" + alIndex + " "
                         + triplet);
               }
@@ -1274,7 +1439,7 @@ 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"))
@@ -1284,26 +1449,26 @@ 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;
-    if (av.scaleAboveWrapped)
+    int hgap = av.getCharHeight();
+    if (av.getScaleAboveWrapped())
     {
-      hgap += av.charHeight;
+      hgap += av.getCharHeight();
     }
 
     int annotationHeight = 0;
-    if (av.showAnnotation)
+    if (av.isShowAnnotation())
     {
-      annotationHeight = annotationPanel.adjustPanelHeight();
+      annotationHeight = getAnnotationPanel().adjustPanelHeight();
     }
 
-    int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+    int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
             + annotationHeight;
 
-    int maxwidth = av.alignment.getWidth();
-    if (av.hasHiddenColumns)
+    int maxwidth = av.getAlignment().getWidth();
+    if (av.hasHiddenColumns())
     {
       maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
     }
@@ -1319,15 +1484,19 @@ 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);
-      av.alignment = null;
+      jalview.structure.StructureSelectionManager ssm = av
+              .getStructureSelectionManager();
+      ssm.removeStructureViewerListener(getSeqPanel(), null);
+      ssm.removeSelectionListener(getSeqPanel());
+      ssm.removeEditListener(av);
+      ssm.removeStructureViewerListener(getSeqPanel(), null);
+      ssm.removeSelectionListener(getSeqPanel());
+      av.setAlignment(null);
       av = null;
     }
     else
@@ -1344,87 +1513,30 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public void updateAnnotation()
   {
-    updateAnnotation(false);
+    updateAnnotation(false, false);
   }
 
   public void updateAnnotation(boolean applyGlobalSettings)
   {
-    // TODO: this should be merged with other annotation update stuff - that
-    // sits on AlignViewport
-    boolean updateCalcs = false;
-    boolean conv = av.isShowGroupConservation();
-    boolean cons = av.isShowGroupConsensus();
-    boolean showprf = av.isShowSequenceLogo();
-    boolean showConsHist = av.isShowConsensusHistogram();
-    boolean normLogo = av.isNormaliseSequenceLogo();
-
-    boolean sortg = true;
-
-    // remove old automatic annotation
-    // add any new annotation
-
-    Vector gr = av.alignment.getGroups(); // OrderedBy(av.alignment.getSequencesArray());
-    // intersect alignment annotation with alignment groups
+    updateAnnotation(applyGlobalSettings, false);
+  }
 
-    AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation();
-    Hashtable oldrfs = new Hashtable();
-    if (aan != null)
-    {
-      for (int an = 0; an < aan.length; an++)
-      {
-        if (aan[an].autoCalculated && aan[an].groupRef != null)
-        {
-          oldrfs.put(aan[an].groupRef, aan[an].groupRef);
-          av.alignment.deleteAnnotation(aan[an]);
-          aan[an] = null;
-        }
-      }
-    }
-    SequenceGroup sg;
-    if (gr != null)
-    {
-      for (int g = 0; g < gr.size(); g++)
-      {
-        updateCalcs = false;
-        sg = (SequenceGroup) gr.elementAt(g);
-        if (applyGlobalSettings || !oldrfs.containsKey(sg))
-        {
-          // set defaults for this group's conservation/consensus
-          sg.setshowSequenceLogo(showprf);
-          sg.setShowConsensusHistogram(showConsHist);
-          sg.setNormaliseSequenceLogo(normLogo);
-        }
-        if (conv)
-        {
-          updateCalcs = true;
-          av.alignment.addAnnotation(sg.getConservationRow(), 0);
-        }
-        if (cons)
-        {
-          updateCalcs = true;
-          av.alignment.addAnnotation(sg.getConsensus(), 0);
-        }
-        // refresh the annotation rows
-        if (updateCalcs)
-        {
-          sg.recalcConservation();
-        }
-      }
-    }
-    oldrfs.clear();
+  public void updateAnnotation(boolean applyGlobalSettings,
+          boolean preserveNewGroupSettings)
+  {
+    av.updateGroupAnnotationSettings(applyGlobalSettings,
+            preserveNewGroupSettings);
     adjustAnnotationHeight();
   }
 
   @Override
   public AlignmentI getAlignment()
   {
-    return av.alignment;
+    return av.getAlignment();
   }
 
-  /**
-   * get the name for this view
-   * @return 
-   */
+
+  @Override
   public String getViewName()
   {
     return av.viewName;
@@ -1432,18 +1544,23 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   /**
    * Make/Unmake this alignment panel the current input focus
+   * 
    * @param b
    */
   public void setSelected(boolean b)
   {
-    try {
+    try
+    {
       alignFrame.setSelected(b);
-      } catch (Exception ex) {};
-      
+    } catch (Exception ex)
+    {
+    }
+    ;
+
     if (b)
     {
       alignFrame.setDisplayedView(this);
-    } 
+    }
   }
 
   @Override
@@ -1455,6 +1572,80 @@ public class AlignmentPanel extends GAlignmentPanel implements
   @Override
   public void raiseOOMWarning(String string, OutOfMemoryError error)
   {
-    new OOMWarning(string,  error, this);
+    new OOMWarning(string, error, this);
+  }
+
+  @Override
+  public jalview.api.FeatureRenderer cloneFeatureRenderer()
+  {
+
+    return new FeatureRenderer(this);
+  }
+  @Override 
+  public jalview.api.FeatureRenderer getFeatureRenderer()
+  {
+    return seqPanel.seqCanvas.getFeatureRenderer();
+  }
+  public void updateFeatureRenderer(jalview.renderer.seqfeatures.FeatureRenderer fr)
+  {
+    fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
+  }
+
+  public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)
+  {
+    if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
+    {
+      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;
   }
 }