X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=541c7c29104d93a80632f0c8e65186ee86f7f1c6;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=8e02a9c3c7cbce6c68e5ada9b25730e11b81d724;hpb=d2f3c59deebfd9ea52b0021ab31467c18b9d2c14;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
old mode 100755
new mode 100644
index 8e02a9c..541c7c2
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,1308 +1,1509 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import jalview.datamodel.*;
-
-import jalview.jbgui.*;
-
-import jalview.schemes.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.print.*;
-
-import java.io.*;
-
-import javax.swing.*;
-
-import org.biojava.dasobert.eventmodel.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class AlignmentPanel extends GAlignmentPanel
-    implements AdjustmentListener, Printable, FeatureListener
-{
-  public AlignViewport av;
-  OverviewPanel overviewPanel;
-  SeqPanel seqPanel;
-  IdPanel idPanel;
-  IdwidthAdjuster idwidthAdjuster;
-
-  /** DOCUMENT ME!! */
-  public AlignFrame alignFrame;
-  ScalePanel scalePanel;
-  AnnotationPanel annotationPanel;
-  AnnotationLabels alabels;
-
-  // this value is set false when selection area being dragged
-  boolean fastPaint = true;
-  int hextent = 0;
-  int vextent = 0;
-
-  /**
-   * 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);
-
-    scalePanel = new ScalePanel(av, this);
-
-    idPanelHolder.add(idPanel, BorderLayout.CENTER);
-    idwidthAdjuster = new IdwidthAdjuster(this);
-    idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
-
-    annotationPanel = new AnnotationPanel(this);
-    alabels = new AnnotationLabels(this);
-
-
-    annotationScroller.setViewportView(annotationPanel);
-    annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
-
-    fontChanged();
-
-    scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
-    seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
-
-    setScrollValues(0, 0);
-
-    adjustAnnotationHeight();
-
-    setAnnotationVisible(av.getShowAnnotation());
-
-    hscroll.addAdjustmentListener(this);
-    vscroll.addAdjustmentListener(this);
-
-    af.addKeyListener(new KeyAdapter()
-    {
-      public void keyPressed(KeyEvent evt)
-      {
-        if(av.cursorMode
-           && evt.getKeyCode()>=KeyEvent.VK_0
-           && evt.getKeyCode()<=KeyEvent.VK_9)
-        {
-          seqPanel.numberPressed(evt.getKeyChar());
-        }
-
-        switch (evt.getKeyCode())
-        {
-          case 27: // escape key
-            av.setSelectionGroup(null);
-            repaint();
-
-            break;
-
-          case KeyEvent.VK_DOWN:
-            if(av.cursorMode)
-            {
-              seqPanel.moveCursor(0,1);
-            }
-            else
-              alignFrame.moveSelectedSequences(false);
-            break;
-
-          case KeyEvent.VK_UP:
-            if (av.cursorMode)
-            {
-              seqPanel.moveCursor(0,-1);
-            }
-            else
-              alignFrame.moveSelectedSequences(true);
-            break;
-
-          case KeyEvent.VK_LEFT:
-            if(av.cursorMode)
-            {
-              seqPanel.moveCursor(-1,0);
-            }
-            break;
-
-          case KeyEvent.VK_RIGHT:
-            if (av.cursorMode)
-            {
-              seqPanel.moveCursor(1,0);
-            }
-            break;
-
-          case KeyEvent.VK_SPACE:
-            if(av.cursorMode)
-            {
-              seqPanel.insertGapAtCursor(evt.isControlDown() || evt.isShiftDown());
-            }
-            break;
-
-          case KeyEvent.VK_DELETE:
-          case KeyEvent.VK_BACK_SPACE:
-            if(!av.cursorMode)
-            {
-              alignFrame.cut_actionPerformed(null);
-              seqPanel.seqCanvas.repaint();
-            }
-            else
-              seqPanel.deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown());
-
-            break;
-
-          case KeyEvent.VK_S:
-            if(av.cursorMode)
-            {
-              seqPanel.setCursorRow();
-            }
-            break;
-          case KeyEvent.VK_C:
-            if(av.cursorMode)
-            {
-              seqPanel.setCursorColumn();
-            }
-            break;
-          case KeyEvent.VK_P:
-            if(av.cursorMode)
-            {
-              seqPanel.setCursorPosition();
-            }
-            break;
-
-          case KeyEvent.VK_ENTER:
-          case KeyEvent.VK_COMMA:
-            if(av.cursorMode)
-            {
-              seqPanel.setCursorRowAndColumn();
-            }
-            break;
-
-          case KeyEvent.VK_Q:
-            if(av.cursorMode)
-            {
-              seqPanel.setSelectionAreaAtCursor(true);
-            }
-            break;
-          case KeyEvent.VK_M:
-            if(av.cursorMode)
-            {
-              seqPanel.setSelectionAreaAtCursor(false);
-            }
-            break;
-
-         case KeyEvent.VK_F2:
-           av.cursorMode = ! av.cursorMode;
-           alignFrame.statusBar.setText("Keyboard editing mode is "+
-               (av.cursorMode ? "on" : "off"));
-           if(av.cursorMode)
-           {
-             seqPanel.seqCanvas.cursorX = av.startRes;
-             seqPanel.seqCanvas.cursorY = av.startSeq;
-           }
-           seqPanel.seqCanvas.repaint();
-           break;
-
-          case KeyEvent.VK_F1:
-            try
-            {
-              ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
-              java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
-              javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
-
-              javax.help.HelpBroker hb = hs.createHelpBroker();
-              hb.setCurrentID("home");
-              hb.setDisplayed(true);
-            }
-            catch (Exception ex)
-            {
-              ex.printStackTrace();
-            }
-            break;
-
-        }
-      }
-    });
-  }
-
-  public void comeBackLater(FeatureEvent evt)
-  {}
-
-  public void newFeatures(FeatureEvent evt)
-  {
-    if (evt.getFeatures().length > 0)
-    {
-      seqPanel.seqCanvas.fr.featuresAdded();
-      repaint();
-    }
-    else
-    {
-      System.out.println("No Features found for "+evt.getDasSource().getNickname());
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void fontChanged()
-  {
-    // set idCanvas bufferedImage to null
-    // to prevent drawing old image
-    FontMetrics fm = getFontMetrics(av.getFont());
-
-    scalePanelHolder.setPreferredSize(new Dimension(10,
-        av.charHeight + fm.getDescent()));
-    idSpaceFillerPanel1.setPreferredSize(new Dimension(10,
-        av.charHeight + fm.getDescent()));
-
-    idPanel.idCanvas.gg = null;
-    seqPanel.seqCanvas.img = null;
-    annotationPanel.adjustPanelHeight();
-
-    Dimension d = calculateIdWidth();
-    d.setSize(d.width + 4, d.height);
-    idPanel.idCanvas.setPreferredSize(d);
-    hscrollFillerPanel.setPreferredSize(d);
-
-    if (av.getWrapAlignment())
-    {
-      int max = av.alignment.getWidth() /
-          seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
-      vscroll.setMaximum(max);
-      vscroll.setUnitIncrement(1);
-      vscroll.setVisibleAmount(1);
-    }
-    else
-    {
-      setScrollValues(av.getStartRes(), av.getStartSeq());
-    }
-
-    if (overviewPanel != null)
-      overviewPanel.setBoxPosition();
-
-    repaint();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Dimension calculateIdWidth()
-  {
-    Container c = new Container();
-
-    FontMetrics fm = c.getFontMetrics(av.font);
-    AlignmentI al = av.getAlignment();
-
-    int i = 0;
-    int idWidth = 0;
-    String id;
-
-    while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null))
-    {
-      SequenceI s = al.getSequenceAt(i);
-
-      id = s.getDisplayId(av.getShowJVSuffix());
-
-      if (fm.stringWidth(id) > idWidth)
-      {
-        idWidth = fm.stringWidth(id);
-      }
-
-      i++;
-    }
-
-    // Also check annotation label widths
-    i = 0;
-
-    if (al.getAlignmentAnnotation() != null)
-    {
-      fm = c.getFontMetrics(alabels.getFont());
-
-      while (i < al.getAlignmentAnnotation().length)
-      {
-        String label = al.getAlignmentAnnotation()[i].label;
-
-        if (fm.stringWidth(label) > idWidth)
-        {
-          idWidth = fm.stringWidth(label);
-        }
-
-        i++;
-      }
-    }
-
-    return new Dimension(idWidth, 12);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param results DOCUMENT ME!
-   */
-  public void highlightSearchResults(SearchResults results)
-  {
-    seqPanel.seqCanvas.highlightSearchResults(results);
-
-    // do we need to scroll the panel?
-    if (results != null)
-    {
-      SequenceI seq = results.getResultSequence(0);
-      int seqIndex = av.alignment.findIndex(seq);
-      int start = seq.findIndex(results.getResultStart(0)) - 1;
-      int end = seq.findIndex(results.getResultEnd(0)) - 1;
-
-      if(!av.wrapAlignment)
-      {
-        if ( (av.getStartRes() > end)  || (av.getEndRes() < start) ||
-           ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
-        {
-          setScrollValues(start, seqIndex);
-        }
-      }
-      else
-      {
-        scrollToWrappedVisible(start);
-      }
-    }
-  }
-
-  void scrollToWrappedVisible(int res)
-  {
-    int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
-    if( res<=av.getStartRes() || res>=(av.getStartRes()+cwidth) )
-    {
-      vscroll.setValue(res / cwidth);
-      av.startRes = vscroll.getValue() * cwidth;
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public OverviewPanel getOverviewPanel()
-  {
-    return overviewPanel;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param op DOCUMENT ME!
-   */
-  public void setOverviewPanel(OverviewPanel op)
-  {
-    overviewPanel = op;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param b DOCUMENT ME!
-   */
-  public void setAnnotationVisible(boolean b)
-  {
-    if (!av.wrapAlignment)
-    {
-      annotationSpaceFillerHolder.setVisible(b);
-      annotationScroller.setVisible(b);
-    }
-    repaint();
-  }
-
-  public void adjustAnnotationHeight()
-  {
-    javax.swing.SwingUtilities.invokeLater(new Runnable()
-    {
-      public void run()
-      {
-          while(alignFrame.getHeight()==0)
-          {
-            Thread.yield();
-          }
-
-        int height = annotationPanel.adjustPanelHeight();
-
-        if (height > alignFrame.getHeight() / 2)
-        {
-          height = alignFrame.getHeight() / 2;
-        }
-
-        annotationScroller.setPreferredSize(
-            new Dimension(annotationScroller.getWidth(),
-                          height));
-
-        annotationSpaceFillerHolder.setPreferredSize(new Dimension(
-            annotationSpaceFillerHolder.getWidth(),
-            height));
-
-        annotationPanel.repaint();
-      }
-    });
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param wrap DOCUMENT ME!
-   */
-  public void setWrapAlignment(boolean wrap)
-  {
-    av.startSeq = 0;
-    scalePanelHolder.setVisible(!wrap);
-    hscroll.setVisible(!wrap);
-    idwidthAdjuster.setVisible(!wrap);
-
-    if (wrap)
-    {
-      annotationScroller.setVisible(false);
-      annotationSpaceFillerHolder.setVisible(false);
-    }
-    else if (av.showAnnotation)
-    {
-      annotationScroller.setVisible(true);
-      annotationSpaceFillerHolder.setVisible(true);
-    }
-
-    idSpaceFillerPanel1.setVisible(!wrap);
-
-    repaint();
-  }
-
-  // return value is true if the scroll is valid
-  public boolean scrollUp(boolean up)
-  {
-    if (up)
-    {
-      if (vscroll.getValue() < 1)
-      {
-        return false;
-      }
-
-      fastPaint = false;
-      vscroll.setValue(vscroll.getValue() - 1);
-    }
-    else
-    {
-      if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
-      {
-        return false;
-      }
-
-      fastPaint = false;
-      vscroll.setValue(vscroll.getValue() + 1);
-    }
-
-    fastPaint = true;
-
-    return true;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param right DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public boolean scrollRight(boolean right)
-  {
-    if (!right)
-    {
-      if (hscroll.getValue() < 1)
-      {
-        return false;
-      }
-
-      fastPaint = false;
-      hscroll.setValue(hscroll.getValue() - 1);
-    }
-    else
-    {
-      if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
-      {
-        return false;
-      }
-
-      fastPaint = false;
-      hscroll.setValue(hscroll.getValue() + 1);
-    }
-
-    fastPaint = true;
-
-    return true;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param x DOCUMENT ME!
-   * @param y DOCUMENT ME!
-   */
-  public void setScrollValues(int x, int y)
-  {
-
-    int width = av.alignment.getWidth();
-    int height = av.alignment.getHeight();
-
-    if(av.hasHiddenColumns)
-     width = av.getColumnSelection().findColumnPosition(width);
-
-    av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) -1);
-
-    hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
-    vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
-
-    if (hextent > width)
-    {
-      hextent = width;
-    }
-
-    if (vextent > height)
-    {
-      vextent = height;
-    }
-
-    if ( (hextent + x) > width)
-    {
-      x = width - hextent;
-    }
-
-    if ( (vextent + y) > height)
-    {
-      y = height - vextent;
-    }
-
-    if (y < 0)
-    {
-      y = 0;
-    }
-
-    if (x < 0)
-    {
-      x = 0;
-    }
-
-    hscroll.setValues(x, hextent, 0, width);
-    vscroll.setValues(y, vextent, 0, height);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void adjustmentValueChanged(AdjustmentEvent evt)
-  {
-    int oldX = av.getStartRes();
-    int oldY = av.getStartSeq();
-
-    if (evt.getSource() == hscroll)
-    {
-      int x = hscroll.getValue();
-      av.setStartRes(x);
-      av.setEndRes( (x +
-                     (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
-    }
-
-    if (evt.getSource() == vscroll)
-    {
-      int offy = vscroll.getValue();
-
-      if (av.getWrapAlignment())
-      {
-        int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
-            seqCanvas.getWidth());
-        av.setStartRes(vscroll.getValue() * rowSize);
-        av.setEndRes( (vscroll.getValue() + 1) * rowSize);
-      }
-      else
-      {
-        av.setStartSeq(offy);
-        av.setEndSeq(offy +
-                     (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
-      }
-    }
-
-    if (overviewPanel != null)
-    {
-      overviewPanel.setBoxPosition();
-    }
-
-    int scrollX = av.startRes - oldX;
-    int scrollY = av.startSeq - oldY;
-
-    if (av.getWrapAlignment() || !fastPaint)
-    {
-      repaint();
-    }
-    else
-    {
-      // Make sure we're not trying to draw a panel
-      // larger than the visible window
-      if(scrollX>av.endRes-av.startRes)
-        scrollX = av.endRes-av.startRes;
-      else if(scrollX<av.startRes-av.endRes)
-        scrollX = av.startRes - av.endRes;
-
-      if(scrollX!=0 || scrollY!=0)
-      {
-        idPanel.idCanvas.fastPaint(scrollY);
-        seqPanel.seqCanvas.fastPaint(scrollX,
-                                     scrollY);
-        scalePanel.repaint();
-
-        if (av.getShowAnnotation())
-        {
-          annotationPanel.fastPaint(scrollX);
-        }
-      }
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   */
-  public void paintComponent(Graphics g)
-  {
-    invalidate();
-
-    Dimension d = idPanel.idCanvas.getPreferredSize();
-    idPanelHolder.setPreferredSize(d);
-    hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
-    validate();
-
-    if (av.getWrapAlignment())
-    {
-      int max = av.alignment.getWidth() /
-          seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +1;
-
-
-      vscroll.setMaximum(max);
-      vscroll.setUnitIncrement(1);
-      vscroll.setVisibleAmount(1);
-    }
-    else
-    {
-      setScrollValues(av.getStartRes(), av.getStartSeq());
-    }
-
-    if( this.getVisibleRect().getBounds() == g.getClipBounds()
-        && overviewPanel != null)
-        overviewPanel.updateOverviewImage();
-
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param pg DOCUMENT ME!
-   * @param pf DOCUMENT ME!
-   * @param pi DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   *
-   * @throws PrinterException DOCUMENT ME!
-   */
-  public int print(Graphics pg, PageFormat pf, int pi)
-      throws PrinterException
-  {
-    pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
-
-    int pwidth = (int) pf.getImageableWidth();
-    int pheight = (int) pf.getImageableHeight();
-
-    if (av.getWrapAlignment())
-    {
-      return printWrappedAlignment(pg, pwidth, pheight, pi);
-    }
-    else
-    {
-      return printUnwrapped(pg, pwidth, pheight, pi);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param pg DOCUMENT ME!
-   * @param pwidth DOCUMENT ME!
-   * @param pheight DOCUMENT ME!
-   * @param pi DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   *
-   * @throws PrinterException DOCUMENT ME!
-   */
-  public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
-      throws PrinterException
-  {
-    int idWidth = calculateIdWidth().width + 4;
-    FontMetrics fm = getFontMetrics(av.getFont());
-    int scaleHeight = av.charHeight + fm.getDescent();
-
-    pg.setColor(Color.white);
-    pg.fillRect(0, 0, pwidth, pheight);
-    pg.setFont(av.getFont());
-
-    ////////////////////////////////////
-    /// 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 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.alignment.getHeight() / totalSeq) + 1) * pheight;
-
-    if (av.showAnnotation)
-    {
-      pagesHigh += annotationPanel.adjustPanelHeight() + 3;
-    }
-
-    pagesHigh /= pheight;
-
-    if (pi >= (pagesWide * pagesHigh))
-    {
-      return Printable.NO_SUCH_PAGE;
-    }
-
-    //draw Scale
-    pg.translate(idWidth, 0);
-    scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
-    pg.translate( -idWidth, scaleHeight);
-
-    ////////////////
-    // Draw the ids
-    Color currentColor = null;
-    Color currentTextColor = null;
-
-    pg.setFont(new Font(av.getFont().getName(),
-                        Font.ITALIC,
-                        av.getFont().getSize()));
-    for (int i = startSeq; i < endSeq; i++)
-    {
-      if ( (av.getSelectionGroup() != null) &&
-          av.getSelectionGroup().sequences.contains(
-              av.getAlignment().getSequenceAt(i)))
-      {
-        currentColor = Color.gray;
-        currentTextColor = Color.black;
-      }
-      else
-      {
-        currentColor = av.getAlignment().getSequenceAt(i).getColor();
-        currentTextColor = Color.black;
-      }
-
-      pg.setColor(currentColor);
-      pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
-                  av.getCharHeight());
-
-      pg.setColor(currentTextColor);
-
-      String string = av.getAlignment().getSequenceAt(i).getDisplayId
-          ( av.getShowJVSuffix());
-
-      pg.drawString(string, 0,
-                    ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
-                    (av.getCharHeight() / 5));
-    }
-
-    pg.setFont(av.getFont());
-
-    // draw main sequence panel
-    pg.translate(idWidth, 0);
-    seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
-
-    if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
-    {
-      pg.translate( -idWidth-3, (endSeq - startSeq) * av.charHeight + 3);
-      alabels.drawComponent( (Graphics2D) pg, idWidth);
-      pg.translate(idWidth+3, 0);
-      annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
-                                    1);
-    }
-
-    return Printable.PAGE_EXISTS;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param pg DOCUMENT ME!
-   * @param pwidth DOCUMENT ME!
-   * @param pheight DOCUMENT ME!
-   * @param pi DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   *
-   * @throws PrinterException DOCUMENT ME!
-   */
-  public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
-                                   int pi)
-      throws PrinterException
-  {
-
-    int annotationHeight = 0;
-    AnnotationLabels labels = null;
-    if (av.showAnnotation)
-    {
-      annotationHeight = annotationPanel.adjustPanelHeight();
-      labels = new AnnotationLabels(av);
-    }
-
-    int hgap = av.charHeight;
-    if (av.scaleAboveWrapped)
-      hgap += av.charHeight;
-
-    int cHeight = av.getAlignment().getHeight() * av.charHeight
-        + hgap
-        + annotationHeight;
-
-    int idWidth = calculateIdWidth().width + 4;
-
-    int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
-        idWidth);
-
-    int totalHeight = cHeight * (av.alignment.getWidth() / resWidth + 1);
-
-    pg.setColor(Color.white);
-    pg.fillRect(0, 0, pwidth, pheight);
-    pg.setFont(av.getFont());
-
-    ////////////////
-    // Draw the ids
-    pg.setColor(Color.black);
-
-    pg.translate(0, -pi * pheight);
-
-    pg.setClip(0, pi * pheight, pwidth, pheight);
-
-    int ypos = hgap;
-    Font italic = new Font(av.getFont().getName(), Font.ITALIC,
-                           av.getFont().getSize());
-    pg.setFont(italic);
-
-    do
-    {
-      for (int i = 0; i < av.alignment.getHeight(); i++)
-      {
-        SequenceI s = av.alignment.getSequenceAt(i);
-        String string = s.getDisplayId( av.getShowJVSuffix());
-
-        pg.drawString(string, 0,
-                      ( (i * av.charHeight) + ypos + av.charHeight) -
-                      (av.charHeight / 5));
-      }
-      if (labels != null)
-      {
-        pg.translate(-3,
-                     ypos +
-                     (av.getAlignment().getHeight() * av.charHeight));
-
-        pg.setFont(av.getFont());
-        labels.drawComponent(pg, idWidth);
-        pg.setFont(italic);
-        pg.translate(+3,
-                     -ypos -
-                     (av.getAlignment().getHeight() * av.charHeight));
-      }
-
-      ypos += cHeight;
-    }
-    while (ypos < totalHeight);
-
-    pg.translate(idWidth, 0);
-
-    seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
-
-    if ( (pi * pheight) < totalHeight)
-    {
-      return Printable.PAGE_EXISTS;
-
-    }
-    else
-    {
-      return Printable.NO_SUCH_PAGE;
-    }
-  }
-
-  void makeAlignmentImage(int type, File file)
-  {
-    int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
-    int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
-    if (idPanel.getWidth() == 0)
-    {
-      width += calculateIdWidth().getWidth() + 4;
-    }
-
-    if (av.getWrapAlignment())
-    {
-      height = getWrappedHeight();
-      if (System.getProperty("java.awt.headless") != null
-          && System.getProperty("java.awt.headless").equals("true"))
-      {
-        width = alignFrame.getWidth() - 22;
-      }
-      else
-
-        width = seqPanel.getWidth() + idPanel.getWidth();
-
-    }
-    else if (av.getShowAnnotation())
-    {
-      height += annotationPanel.adjustPanelHeight() + 3;
-    }
-
-    jalview.util.ImageMaker im;
-    if(type==jalview.util.ImageMaker.PNG)
-      im  = new jalview.util.ImageMaker(this,
-                                        jalview.util.ImageMaker.PNG,
-                                        "Create PNG image from alignment",
-                                        width, height, file, null);
-    else
-      im = new jalview.util.ImageMaker(this,
-                                        jalview.util.ImageMaker.EPS,
-                                       "Create EPS file from alignment",
-                                        width, height, file, alignFrame.getTitle() );
-
-    try
-    {
-      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)
-    {
-      System.out.println("########################\n"
-                         + "OUT OF MEMORY " + file + "\n"
-                         + "########################");
-
-      JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                            "Out of Memory Creating Image!!"
-                                            +
-                                            "\nSee help files for increasing Java Virtual Machine memory."
-                                            , "Out of memory",
-                                            JOptionPane.WARNING_MESSAGE);
-      System.out.println("Create IMAGE: " + err);
-      System.gc();
-
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
-  /**
-   * DOCUMENT ME!
-   */
-  public void makeEPS(File epsFile)
-  {
-    makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void makePNG(File pngFile)
-  {
-    makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
-  }
-
-  public void makePNGImageMap(File imgMapFile, String imageName)
-  {
-    ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
-    //////////////////////////////////////////////
-    int idWidth = calculateIdWidth().width + 4;
-    FontMetrics fm = getFontMetrics(av.getFont());
-    int scaleHeight = av.charHeight + fm.getDescent();
-
-    // Gen image map
-    //////////////////////////////////
-    if (imgMapFile != null)
-    {
-      try
-      {
-        int s, sSize = av.alignment.getHeight(),
-            res, alwidth = av.alignment.getWidth(), g, gSize, f, fSize, sy;
-        StringBuffer text = new StringBuffer();
-        PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
-        out.println(jalview.io.HTMLOutput.getImageMapHTML());
-        out.println("<img src=\"" + imageName +
-                    "\" border=\"0\" usemap=\"#Map\" >"
-                    + "<map name=\"Map\">");
-
-        for (s = 0; s < sSize; s++)
-        {
-          sy = s * av.charHeight + scaleHeight;
-
-          SequenceI seq = av.alignment.getSequenceAt(s);
-          SequenceFeature [] features = seq.getDatasetSequence().getSequenceFeatures();
-          SequenceGroup[] groups = av.alignment.findAllGroups(seq);
-          for(res =0; res<alwidth; res++)
-          {
-            text = new StringBuffer();
-            Object obj = null;
-            if(av.alignment.isNucleotide())
-              obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)+"" );
-            else
-              obj = ResidueProperties.aa2Triplet.get(
-                    seq.getCharAt(res) + "");
-
-              if (obj == null)
-                  continue;
-
-            String triplet = obj.toString();
-            int alIndex = seq.findPosition(res);
-            gSize = groups.length;
-            for (g = 0; g < gSize; g++)
-            {
-              if(text.length()<1)
-              {
-                text.append("<area shape=\"rect\" coords=\""
-                  + (idWidth + res * av.charWidth) + ","
-                  + sy + ","
-                  + (idWidth + (res + 1) * av.charWidth) + ","
-                  + (av.charHeight + sy) + "\""
-                  + " onMouseOver=\"toolTip('"
-                  + alIndex + " " + triplet );
-              }
-
-              if(groups[g].getStartRes()<res && groups[g].getEndRes()>res)
-                text.append("<br><em>" + groups[g].getName() + "</em>");
-            }
-
-            if (features != null)
-            {
-              if(text.length()<1)
-              {
-                text.append("<area shape=\"rect\" coords=\""
-                  + (idWidth + res * av.charWidth) + ","
-                  + sy + ","
-                  + (idWidth + (res + 1) * av.charWidth) + ","
-                  + (av.charHeight + sy) + "\""
-                  + " onMouseOver=\"toolTip('"
-                  + alIndex + " " + triplet );
-              }
-                fSize = features.length;
-                for (f = 0; f < fSize; f++)
-                {
-
-                  if ( (features[f].getBegin() <= seq.findPosition(res)) &&
-                      (features[f].getEnd() >= seq.findPosition(res)))
-                  {
-                    if (features[f].getType().equals("disulfide bond"))
-                    {
-                      if (features[f].getBegin() == seq.findPosition(res)
-                          || features[f].getEnd() == seq.findPosition(res))
-                      {
-                        text.append("<br>disulfide bond " + features[f].getBegin() + ":" +
-                                       features[f].getEnd());
-                      }
-                    }
-                    else
-                    {
-                      text.append("<br>");
-                      text.append(features[f].getType());
-                      if (features[f].getDescription() != null && !features[f].getType().equals(features[f].getDescription()))
-                        text.append(" " + features[f].getDescription());
-
-                      if (features[f].getValue("status") != null )
-                      {
-                        text.append(" (" + features[f].getValue("status") + ")");
-                      }
-                    }
-                  }
-
-                }
-              }
-              if(text.length()>1)
-              {
-                text.append("')\"; onMouseOut=\"toolTip()\";  href=\"#\">");
-                out.println(text.toString());
-              }
-            }
-          }
-        out.println("</map></body></html>");
-        out.close();
-
-      }
-      catch (Exception ex)
-      {
-        ex.printStackTrace();
-      }
-    } ///////////END OF IMAGE MAP
-
-  }
-
-  int getWrappedHeight()
-  {
-    int seqPanelWidth = seqPanel.seqCanvas.getWidth();
-
-    //If headless, seqPanel will have 0 width
-    if (System.getProperty("java.awt.headless") != null
-              && System.getProperty("java.awt.headless").equals("true"))
-    {
-      int idWidth = calculateIdWidth().width + 4;
-      seqPanelWidth = alignFrame.getWidth() - idWidth;
-    }
-
-    int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(
-        seqPanelWidth
-          );
-
-    int hgap = av.charHeight;
-    if (av.scaleAboveWrapped)
-      hgap += av.charHeight;
-
-    int annotationHeight = 0;
-    if (av.showAnnotation)
-    {
-      annotationHeight = annotationPanel.adjustPanelHeight();
-    }
-
-    int cHeight = av.getAlignment().getHeight() * av.charHeight
-        + hgap
-        + annotationHeight;
-
-    int height = ( (av.alignment.getWidth() / chunkWidth) + 1) * cHeight;
-
-    return height;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @author $author$
-   * @version $Revision$
-   */
-  class Preview
-      extends JFrame
-  {
-    /**
-     * Creates a new Preview object.
-     *
-     * @param image DOCUMENT ME!
-     */
-    public Preview(Image image)
-    {
-      setResizable(true);
-      setSize(image.getWidth(this), image.getHeight(this));
-      setVisible(true);
-      getContentPane().setLayout(new BorderLayout());
-      getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);
-      validate();
-      repaint();
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @author $author$
-   * @version $Revision$
-   */
-  class PreviewPanel
-      extends JPanel
-  {
-    Image image;
-
-    /**
-     * Creates a new PreviewPanel object.
-     *
-     * @param image DOCUMENT ME!
-     */
-    public PreviewPanel(Image image)
-    {
-      this.image = image;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g DOCUMENT ME!
-     */
-    public void paintComponent(Graphics g)
-    {
-      if (image != null)
-      {
-        g.drawImage(image, 0, 0, this);
-      }
-      else
-      {
-        System.out.println("DEBUG:image is null");
-      }
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import java.beans.*;
+import java.io.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.print.*;
+import javax.swing.*;
+
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.datamodel.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
+import jalview.structure.StructureSelectionManager;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision: 1.161 $
+ */
+public class AlignmentPanel extends GAlignmentPanel implements
+        AdjustmentListener, Printable, AlignmentViewPanel
+{
+  public AlignViewport av;
+
+  OverviewPanel overviewPanel;
+
+  SeqPanel seqPanel;
+
+  IdPanel idPanel;
+
+  IdwidthAdjuster idwidthAdjuster;
+
+  /** DOCUMENT ME!! */
+  public AlignFrame alignFrame;
+
+  ScalePanel scalePanel;
+
+  AnnotationPanel annotationPanel;
+
+  AnnotationLabels alabels;
+
+  // this value is set false when selection area being dragged
+  boolean fastPaint = true;
+
+  int hextent = 0;
+
+  int vextent = 0;
+
+  /**
+   * 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);
+
+    scalePanel = new ScalePanel(av, this);
+
+    idPanelHolder.add(idPanel, BorderLayout.CENTER);
+    idwidthAdjuster = new IdwidthAdjuster(this);
+    idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
+
+    annotationPanel = new AnnotationPanel(this);
+    alabels = new AnnotationLabels(this);
+
+    annotationScroller.setViewportView(annotationPanel);
+    annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
+
+    scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
+    seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
+
+    setScrollValues(0, 0);
+
+    setAnnotationVisible(av.getShowAnnotation());
+
+    hscroll.addAdjustmentListener(this);
+    vscroll.addAdjustmentListener(this);
+
+    final AlignmentPanel ap = this;
+    av.addPropertyChangeListener(new PropertyChangeListener()
+    {
+      public void propertyChange(PropertyChangeEvent evt)
+      {
+        if (evt.getPropertyName().equals("alignment"))
+        {
+          PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
+          alignmentChanged();
+        }
+      }
+    });
+    fontChanged();
+    adjustAnnotationHeight();
+
+  }
+
+  public void alignmentChanged()
+  {
+    av.alignmentChanged(this);
+
+    alignFrame.updateEditMenuBar();
+
+    paintAlignment(true);
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void fontChanged()
+  {
+    // set idCanvas bufferedImage to null
+    // to prevent drawing old image
+    FontMetrics fm = getFontMetrics(av.getFont());
+
+    scalePanelHolder.setPreferredSize(new Dimension(10, av.charHeight
+            + fm.getDescent()));
+    idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av.charHeight
+            + fm.getDescent()));
+
+    idPanel.idCanvas.gg = null;
+    seqPanel.seqCanvas.img = null;
+    annotationPanel.adjustPanelHeight();
+
+    Dimension d = calculateIdWidth();
+    d.setSize(d.width + 4, d.height);
+    idPanel.idCanvas.setPreferredSize(d);
+    hscrollFillerPanel.setPreferredSize(d);
+
+    if (overviewPanel != null)
+    {
+      overviewPanel.setBoxPosition();
+    }
+
+    repaint();
+  }
+
+  /**
+   * Calculate the width of the alignment labels based on the displayed names
+   * and any bounds on label width set in preferences.
+   * 
+   * @return Dimension giving the maximum width of the alignment label panel
+   *         that should be used.
+   */
+  public Dimension calculateIdWidth()
+  {
+    // calculate sensible default width when no preference is available
+
+    int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
+    int maxwidth = Math.max(20,
+            Math.min(afwidth - 200, (int) 2 * afwidth / 3));
+    return calculateIdWidth(maxwidth);
+  }
+
+  /**
+   * 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 i = 0;
+    int idWidth = 0;
+    String id;
+
+    while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
+    {
+      SequenceI s = al.getSequenceAt(i);
+
+      id = s.getDisplayId(av.getShowJVSuffix());
+
+      if (fm.stringWidth(id) > idWidth)
+      {
+        idWidth = fm.stringWidth(id);
+      }
+
+      i++;
+    }
+
+    // Also check annotation label widths
+    i = 0;
+
+    if (al.getAlignmentAnnotation() != null)
+    {
+      fm = c.getFontMetrics(alabels.getFont());
+
+      while (i < al.getAlignmentAnnotation().length)
+      {
+        String label = al.getAlignmentAnnotation()[i].label;
+
+        if (fm.stringWidth(label) > idWidth)
+        {
+          idWidth = fm.stringWidth(label);
+        }
+
+        i++;
+      }
+    }
+
+    return new Dimension(maxwidth < 0 ? idWidth : Math.min(maxwidth,
+            idWidth), 12);
+  }
+
+  /**
+   * Highlight the given results on the alignment.
+   * 
+   */
+  public void highlightSearchResults(SearchResults results)
+  {
+    scrollToPosition(results);
+    seqPanel.seqCanvas.highlightSearchResults(results);
+  }
+
+  /**
+   * scroll the view to show the position of the highlighted region in results
+   * (if any) and redraw the overview
+   * 
+   * @param results
+   */
+  public boolean scrollToPosition(SearchResults results)
+  {
+    return scrollToPosition(results, true);
+  }
+
+  /**
+   * scroll the view to show the position of the highlighted region in results
+   * (if any)
+   * 
+   * @param results
+   * @param redrawOverview
+   *          - when set, the overview will be recalculated (takes longer)
+   * @return false if results were not found
+   */
+  public boolean scrollToPosition(SearchResults results,
+          boolean redrawOverview)
+  {
+    int startv, endv, starts, ends, width;
+    // TODO: properly locate search results in view when large numbers of hidden
+    // columns exist before highlighted region
+    // do we need to scroll the panel?
+    // TODO: tons of nullpointereexceptions raised here.
+    if (results != null && results.getSize() > 0 && av != null
+            && av.getAlignment() != null)
+    {
+      int seqIndex = av.getAlignment().findIndex(results);
+      if (seqIndex == -1)
+      {
+        return false;
+      }
+      SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
+
+      int[] r = results.getResults(seq, 0, av.getAlignment().getWidth());
+      if (r == null)
+      {
+        return false;
+      }
+      int start = r[0];
+      int end = r[1];
+      // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); //
+      // DEBUG
+      if (start < 0)
+      {
+        return false;
+      }
+      if (end == seq.getEnd())
+      {
+        return false;
+      }
+      if (av.hasHiddenColumns())
+      {
+        start = av.getColumnSelection().findColumnPosition(start);
+        end = av.getColumnSelection().findColumnPosition(end);
+        if (start == end)
+        {
+          if (!av.getColumnSelection().isVisible(r[0]))
+          {
+            // don't scroll - position isn't visible
+            return false;
+          }
+        }
+      }
+      if (!av.wrapAlignment)
+      {
+        if ((startv = av.getStartRes()) >= start)
+        {
+          setScrollValues(start - 1, seqIndex);
+        }
+        else if ((endv = av.getEndRes()) <= end)
+        {
+          setScrollValues(startv + 1 + end - endv, seqIndex);
+        }
+        else if ((starts = av.getStartSeq()) > seqIndex)
+        {
+          setScrollValues(av.getStartRes(), seqIndex);
+        }
+        else if ((ends = av.getEndSeq()) <= seqIndex)
+        {
+          setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
+        }
+      }
+      else
+      {
+        scrollToWrappedVisible(start);
+      }
+    }
+    if (redrawOverview && overviewPanel != null)
+    {
+      overviewPanel.setBoxPosition();
+    }
+    paintAlignment(redrawOverview);
+    return true;
+  }
+
+  void scrollToWrappedVisible(int res)
+  {
+    int cwidth = seqPanel.seqCanvas
+            .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+    if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth))
+    {
+      vscroll.setValue((res / cwidth));
+      av.startRes = vscroll.getValue() * cwidth;
+    }
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public OverviewPanel getOverviewPanel()
+  {
+    return overviewPanel;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param op
+   *          DOCUMENT ME!
+   */
+  public void setOverviewPanel(OverviewPanel op)
+  {
+    overviewPanel = op;
+  }
+
+  /**
+   * 
+   * @param b
+   *          Hide or show annotation panel
+   * 
+   */
+  public void setAnnotationVisible(boolean b)
+  {
+    if (!av.wrapAlignment)
+    {
+      annotationSpaceFillerHolder.setVisible(b);
+      annotationScroller.setVisible(b);
+    }
+    repaint();
+  }
+
+  /**
+   * automatically adjust annotation panel height for new annotation whilst
+   * ensuring the alignment is still visible.
+   */
+  public void adjustAnnotationHeight()
+  {
+    // TODO: display vertical annotation scrollbar if necessary
+    // this is called after loading new annotation onto alignment
+    if (alignFrame.getHeight() == 0)
+    {
+      System.out.println("NEEDS FIXING");
+    }
+    validateAnnotationDimensions(true);
+    addNotify();
+    paintAlignment(true);
+  }
+
+  /**
+   * calculate the annotation dimensions and refresh slider values accordingly.
+   * 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;
+    }
+    if (!adjustPanelHeight)
+    {
+      // maintain same window layout whilst updating sliders
+      height = annotationScroller.getSize().height;
+    }
+    hscroll.addNotify();
+
+    annotationScroller.setPreferredSize(new Dimension(annotationScroller
+            .getWidth(), height));
+
+    annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+            annotationSpaceFillerHolder.getWidth(), height));
+    annotationScroller.validate();// repaint();
+    annotationScroller.addNotify();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param wrap
+   *          DOCUMENT ME!
+   */
+  public void setWrapAlignment(boolean wrap)
+  {
+    av.startSeq = 0;
+    scalePanelHolder.setVisible(!wrap);
+    hscroll.setVisible(!wrap);
+    idwidthAdjuster.setVisible(!wrap);
+
+    if (wrap)
+    {
+      annotationScroller.setVisible(false);
+      annotationSpaceFillerHolder.setVisible(false);
+    }
+    else if (av.showAnnotation)
+    {
+      annotationScroller.setVisible(true);
+      annotationSpaceFillerHolder.setVisible(true);
+    }
+
+    idSpaceFillerPanel1.setVisible(!wrap);
+
+    repaint();
+  }
+
+  // return value is true if the scroll is valid
+  public boolean scrollUp(boolean up)
+  {
+    if (up)
+    {
+      if (vscroll.getValue() < 1)
+      {
+        return false;
+      }
+
+      fastPaint = false;
+      vscroll.setValue(vscroll.getValue() - 1);
+    }
+    else
+    {
+      if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
+      {
+        return false;
+      }
+
+      fastPaint = false;
+      vscroll.setValue(vscroll.getValue() + 1);
+    }
+
+    fastPaint = true;
+
+    return true;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param right
+   *          DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean scrollRight(boolean right)
+  {
+    if (!right)
+    {
+      if (hscroll.getValue() < 1)
+      {
+        return false;
+      }
+
+      fastPaint = false;
+      hscroll.setValue(hscroll.getValue() - 1);
+    }
+    else
+    {
+      if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
+      {
+        return false;
+      }
+
+      fastPaint = false;
+      hscroll.setValue(hscroll.getValue() + 1);
+    }
+
+    fastPaint = true;
+
+    return true;
+  }
+
+  /**
+   * 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
+   * 
+   */
+  public void setScrollValues(int x, int y)
+  {
+    // System.err.println("Scroll to "+x+","+y);
+    if (av == null || av.getAlignment() == null)
+    {
+      return;
+    }
+    int width = av.getAlignment().getWidth();
+    int height = av.getAlignment().getHeight();
+
+    if (av.hasHiddenColumns())
+    {
+      width = av.getColumnSelection().findColumnPosition(width);
+    }
+
+    av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1);
+
+    hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
+    vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
+
+    if (hextent > width)
+    {
+      hextent = width;
+    }
+
+    if (vextent > height)
+    {
+      vextent = height;
+    }
+
+    if ((hextent + x) > width)
+    {
+      x = width - hextent;
+    }
+
+    if ((vextent + y) > height)
+    {
+      y = height - vextent;
+    }
+
+    if (y < 0)
+    {
+      y = 0;
+    }
+
+    if (x < 0)
+    {
+      x = 0;
+    }
+
+    hscroll.setValues(x, hextent, 0, width);
+    vscroll.setValues(y, vextent, 0, height);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *          DOCUMENT ME!
+   */
+  public void adjustmentValueChanged(AdjustmentEvent evt)
+  {
+
+    int oldX = av.getStartRes();
+    int oldY = av.getStartSeq();
+
+    if (evt.getSource() == hscroll)
+    {
+      int x = hscroll.getValue();
+      av.setStartRes(x);
+      av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
+    }
+
+    if (evt.getSource() == vscroll)
+    {
+      int offy = vscroll.getValue();
+
+      if (av.getWrapAlignment())
+      {
+        if (offy > -1)
+        {
+          int rowSize = seqPanel.seqCanvas
+                  .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+          av.setStartRes(offy * rowSize);
+          av.setEndRes((offy + 1) * rowSize);
+        }
+        else
+        {
+          // This is only called if file loaded is a jar file that
+          // was wrapped when saved and user has wrap alignment true
+          // as preference setting
+          SwingUtilities.invokeLater(new Runnable()
+          {
+            public void run()
+            {
+              setScrollValues(av.getStartRes(), av.getStartSeq());
+            }
+          });
+        }
+      }
+      else
+      {
+        av.setStartSeq(offy);
+        av.setEndSeq(offy
+                + (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
+      }
+    }
+
+    if (overviewPanel != null)
+    {
+      overviewPanel.setBoxPosition();
+    }
+
+    int scrollX = av.startRes - oldX;
+    int scrollY = av.startSeq - oldY;
+
+    if (av.getWrapAlignment() || !fastPaint)
+    {
+      repaint();
+    }
+    else
+    {
+      // Make sure we're not trying to draw a panel
+      // larger than the visible window
+      if (scrollX > av.endRes - av.startRes)
+      {
+        scrollX = av.endRes - av.startRes;
+      }
+      else if (scrollX < av.startRes - av.endRes)
+      {
+        scrollX = av.startRes - av.endRes;
+      }
+
+      if (scrollX != 0 || scrollY != 0)
+      {
+        idPanel.idCanvas.fastPaint(scrollY);
+        seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
+        scalePanel.repaint();
+
+        if (av.getShowAnnotation() && scrollX!=0)
+        {
+          annotationPanel.fastPaint(scrollX);
+        }
+      }
+    }
+  }
+
+  public void paintAlignment(boolean updateOverview)
+  {
+    repaint();
+
+    if (updateOverview)
+    {
+      av.getStructureSelectionManager().sequenceColoursChanged(this);
+
+      if (overviewPanel != null)
+      {
+        overviewPanel.updateOverviewImage();
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param g
+   *          DOCUMENT ME!
+   */
+  public void paintComponent(Graphics g)
+  {
+    invalidate();
+
+    Dimension d = idPanel.idCanvas.getPreferredSize();
+    idPanelHolder.setPreferredSize(d);
+    hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
+    validate();
+
+    if (av.getWrapAlignment())
+    {
+      int maxwidth = av.getAlignment().getWidth();
+
+      if (av.hasHiddenColumns())
+      {
+        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      }
+
+      int canvasWidth = seqPanel.seqCanvas
+              .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+      if (canvasWidth > 0)
+      {
+        int max = maxwidth
+                / seqPanel.seqCanvas
+                        .getWrappedCanvasWidth(seqPanel.seqCanvas
+                                .getWidth()) + 1;
+        vscroll.setMaximum(max);
+        vscroll.setUnitIncrement(1);
+        vscroll.setVisibleAmount(1);
+      }
+    }
+    else
+    {
+      setScrollValues(av.getStartRes(), av.getStartSeq());
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param pg
+   *          DOCUMENT ME!
+   * @param pf
+   *          DOCUMENT ME!
+   * @param pi
+   *          DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   * 
+   * @throws PrinterException
+   *           DOCUMENT ME!
+   */
+  public int print(Graphics pg, PageFormat pf, int pi)
+          throws PrinterException
+  {
+    pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
+
+    int pwidth = (int) pf.getImageableWidth();
+    int pheight = (int) pf.getImageableHeight();
+
+    if (av.getWrapAlignment())
+    {
+      return printWrappedAlignment(pg, pwidth, pheight, pi);
+    }
+    else
+    {
+      return printUnwrapped(pg, pwidth, pheight, pi);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param pg
+   *          DOCUMENT ME!
+   * @param pwidth
+   *          DOCUMENT ME!
+   * @param pheight
+   *          DOCUMENT ME!
+   * @param pi
+   *          DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   * 
+   * @throws PrinterException
+   *           DOCUMENT ME!
+   */
+  public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
+          throws PrinterException
+  {
+    int idWidth = getVisibleIdWidth(false);
+    FontMetrics fm = getFontMetrics(av.getFont());
+    int scaleHeight = av.charHeight + fm.getDescent();
+
+    pg.setColor(Color.white);
+    pg.fillRect(0, 0, pwidth, pheight);
+    pg.setFont(av.getFont());
+
+    // //////////////////////////////////
+    // / 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 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.showAnnotation)
+    {
+      pagesHigh += annotationPanel.adjustPanelHeight() + 3;
+    }
+
+    pagesHigh /= pheight;
+
+    if (pi >= (pagesWide * pagesHigh))
+    {
+      return Printable.NO_SUCH_PAGE;
+    }
+
+    // draw Scale
+    pg.translate(idWidth, 0);
+    scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth,
+            scaleHeight);
+    pg.translate(-idWidth, scaleHeight);
+
+    // //////////////
+    // Draw the ids
+    Color currentColor = null;
+    Color currentTextColor = null;
+
+    pg.setFont(idPanel.idCanvas.idfont);
+
+    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.setColor(currentColor);
+      pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
+              av.getCharHeight());
+
+      pg.setColor(currentTextColor);
+
+      int xPos = 0;
+      if (av.rightAlignIds)
+      {
+        fm = pg.getFontMetrics();
+        xPos = idWidth
+                - fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix()))
+                - 4;
+      }
+
+      pg.drawString(
+              seq.getDisplayId(av.getShowJVSuffix()),
+              xPos,
+              (((i - startSeq) * av.charHeight) + av.getCharHeight())
+                      - (av.getCharHeight() / 5));
+    }
+
+    pg.setFont(av.getFont());
+
+    // draw main sequence panel
+    pg.translate(idWidth, 0);
+    seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
+
+    if (av.showAnnotation && (endSeq == av.getAlignment().getHeight()))
+    {
+      // draw annotation - need to offset for current scroll position
+      int offset = -alabels.scrollOffset;
+      pg.translate(0, offset);
+      pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
+      alabels.drawComponent((Graphics2D) pg, idWidth);
+      pg.translate(idWidth + 3, 0);
+      annotationPanel.renderer.drawComponent(annotationPanel, av,
+              (Graphics2D) pg, -1, startRes, endRes + 1);
+      pg.translate(0, -offset);
+    }
+
+    return Printable.PAGE_EXISTS;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param pg
+   *          DOCUMENT ME!
+   * @param pwidth
+   *          DOCUMENT ME!
+   * @param pheight
+   *          DOCUMENT ME!
+   * @param pi
+   *          DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   * 
+   * @throws PrinterException
+   *           DOCUMENT ME!
+   */
+  public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
+          int pi) throws PrinterException
+  {
+
+    int annotationHeight = 0;
+    AnnotationLabels labels = null;
+    if (av.showAnnotation)
+    {
+      annotationHeight = annotationPanel.adjustPanelHeight();
+      labels = new AnnotationLabels(av);
+    }
+
+    int hgap = av.charHeight;
+    if (av.scaleAboveWrapped)
+    {
+      hgap += av.charHeight;
+    }
+
+    int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+            + annotationHeight;
+
+    int idWidth = getVisibleIdWidth(false);
+
+    int maxwidth = av.getAlignment().getWidth();
+    if (av.hasHiddenColumns())
+    {
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+    }
+
+    int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth
+            - idWidth);
+
+    int totalHeight = cHeight * (maxwidth / resWidth + 1);
+
+    pg.setColor(Color.white);
+    pg.fillRect(0, 0, pwidth, pheight);
+    pg.setFont(av.getFont());
+
+    // //////////////
+    // Draw the ids
+    pg.setColor(Color.black);
+
+    pg.translate(0, -pi * pheight);
+
+    pg.setClip(0, pi * pheight, pwidth, pheight);
+
+    int ypos = hgap;
+
+    do
+    {
+      for (int i = 0; i < av.getAlignment().getHeight(); i++)
+      {
+        pg.setFont(idPanel.idCanvas.idfont);
+        SequenceI s = av.getAlignment().getSequenceAt(i);
+        String string = s.getDisplayId(av.getShowJVSuffix());
+        int xPos = 0;
+        if (av.rightAlignIds)
+        {
+          FontMetrics fm = pg.getFontMetrics();
+          xPos = idWidth - fm.stringWidth(string) - 4;
+        }
+        pg.drawString(string, xPos,
+                ((i * av.charHeight) + ypos + av.charHeight)
+                        - (av.charHeight / 5));
+      }
+      if (labels != null)
+      {
+        pg.translate(-3, ypos
+                + (av.getAlignment().getHeight() * av.charHeight));
+
+        pg.setFont(av.getFont());
+        labels.drawComponent(pg, idWidth);
+        pg.translate(+3, -ypos
+                - (av.getAlignment().getHeight() * av.charHeight));
+      }
+
+      ypos += cHeight;
+    } while (ypos < totalHeight);
+
+    pg.translate(idWidth, 0);
+
+    seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight,
+            0);
+
+    if ((pi * pheight) < totalHeight)
+    {
+      return Printable.PAGE_EXISTS;
+
+    }
+    else
+    {
+      return Printable.NO_SUCH_PAGE;
+    }
+  }
+
+  /**
+   * get current sequence ID panel width, or nominal value if panel were to be
+   * displayed using default settings
+   * 
+   * @return
+   */
+  int getVisibleIdWidth()
+  {
+    return getVisibleIdWidth(true);
+  }
+
+  /**
+   * 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
+   */
+  int getVisibleIdWidth(boolean onscreen)
+  {
+    // see if rendering offscreen - check preferences and calc width accordingly
+    if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
+    {
+      return calculateIdWidth(-1).width + 4;
+    }
+    Integer idwidth = null;
+    if (onscreen
+            || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
+    {
+      return (idPanel.getWidth() > 0 ? idPanel.getWidth()
+              : calculateIdWidth().width + 4);
+    }
+    return idwidth.intValue() + 4;
+  }
+
+  void makeAlignmentImage(int type, File file)
+  {
+    long progress = System.currentTimeMillis();
+    boolean headless = (System.getProperty("java.awt.headless") != null
+            && System.getProperty("java.awt.headless").equals("true"));
+    if (alignFrame != null && !headless)
+    {
+      alignFrame.setProgressBar("Saving "
+              + (type == jalview.util.ImageMaker.PNG ? "PNG image"
+                      : "EPS file"), progress);
+    }
+    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;
+      }
+
+      try
+      {
+
+        jalview.util.ImageMaker im;
+        final String imageAction, imageTitle;
+        if (type == jalview.util.ImageMaker.PNG)
+        {
+          imageAction = "Create PNG image from alignment";
+          imageTitle = null;
+        }
+        else
+        {
+          imageAction = "Create EPS file from alignment";
+          imageTitle = alignFrame.getTitle();
+        }
+        im = new jalview.util.ImageMaker(this, type, imageAction, width,
+                height, file, imageTitle);
+        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)
+      {
+        ex.printStackTrace();
+      }
+    } finally
+    {
+      if (alignFrame != null && !headless)
+      {
+        alignFrame.setProgressBar("Export complete.", progress);
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void makeEPS(File epsFile)
+  {
+    makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void makePNG(File pngFile)
+  {
+    makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
+  }
+
+  public void makePNGImageMap(File imgMapFile, String imageName)
+  {
+    // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
+    // ////////////////////////////////////////////
+    int idWidth = getVisibleIdWidth(false);
+    FontMetrics fm = getFontMetrics(av.getFont());
+    int scaleHeight = av.charHeight + fm.getDescent();
+
+    // Gen image map
+    // ////////////////////////////////
+    if (imgMapFile != null)
+    {
+      try
+      {
+        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());
+        out.println("<img src=\"" + imageName
+                + "\" border=\"0\" usemap=\"#Map\" >"
+                + "<map name=\"Map\">");
+
+        for (s = 0; s < sSize; s++)
+        {
+          sy = s * av.charHeight + scaleHeight;
+
+          SequenceI seq = av.getAlignment().getSequenceAt(s);
+          SequenceFeature[] features = seq.getDatasetSequence()
+                  .getSequenceFeatures();
+          SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
+          for (res = 0; res < alwidth; res++)
+          {
+            text = new StringBuffer();
+            Object obj = null;
+            if (av.getAlignment().isNucleotide())
+            {
+              obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)
+                      + "");
+            }
+            else
+            {
+              obj = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
+                      + "");
+            }
+
+            if (obj == null)
+            {
+              continue;
+            }
+
+            String triplet = obj.toString();
+            int alIndex = seq.findPosition(res);
+            gSize = groups.length;
+            for (g = 0; g < gSize; g++)
+            {
+              if (text.length() < 1)
+              {
+                text.append("<area shape=\"rect\" coords=\""
+                        + (idWidth + res * av.charWidth) + "," + sy + ","
+                        + (idWidth + (res + 1) * av.charWidth) + ","
+                        + (av.charHeight + sy) + "\""
+                        + " onMouseOver=\"toolTip('" + alIndex + " "
+                        + triplet);
+              }
+
+              if (groups[g].getStartRes() < res
+                      && groups[g].getEndRes() > res)
+              {
+                text.append("<br><em>" + groups[g].getName() + "</em>");
+              }
+            }
+
+            if (features != null)
+            {
+              if (text.length() < 1)
+              {
+                text.append("<area shape=\"rect\" coords=\""
+                        + (idWidth + res * av.charWidth) + "," + sy + ","
+                        + (idWidth + (res + 1) * av.charWidth) + ","
+                        + (av.charHeight + sy) + "\""
+                        + " onMouseOver=\"toolTip('" + alIndex + " "
+                        + triplet);
+              }
+              fSize = features.length;
+              for (f = 0; f < fSize; f++)
+              {
+
+                if ((features[f].getBegin() <= seq.findPosition(res))
+                        && (features[f].getEnd() >= seq.findPosition(res)))
+                {
+                  if (features[f].getType().equals("disulfide bond"))
+                  {
+                    if (features[f].getBegin() == seq.findPosition(res)
+                            || features[f].getEnd() == seq
+                                    .findPosition(res))
+                    {
+                      text.append("<br>disulfide bond "
+                              + features[f].getBegin() + ":"
+                              + features[f].getEnd());
+                    }
+                  }
+                  else
+                  {
+                    text.append("<br>");
+                    text.append(features[f].getType());
+                    if (features[f].getDescription() != null
+                            && !features[f].getType().equals(
+                                    features[f].getDescription()))
+                    {
+                      text.append(" " + features[f].getDescription());
+                    }
+
+                    if (features[f].getValue("status") != null)
+                    {
+                      text.append(" (" + features[f].getValue("status")
+                              + ")");
+                    }
+                  }
+                }
+
+              }
+            }
+            if (text.length() > 1)
+            {
+              text.append("')\"; onMouseOut=\"toolTip()\";  href=\"#\">");
+              out.println(text.toString());
+            }
+          }
+        }
+        out.println("</map></body></html>");
+        out.close();
+
+      } catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    } // /////////END OF IMAGE MAP
+
+  }
+
+  int getWrappedHeight()
+  {
+    int seqPanelWidth = seqPanel.seqCanvas.getWidth();
+
+    if (System.getProperty("java.awt.headless") != null
+            && System.getProperty("java.awt.headless").equals("true"))
+    {
+      seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
+              - vscroll.getPreferredSize().width
+              - alignFrame.getInsets().left - alignFrame.getInsets().right;
+    }
+
+    int chunkWidth = seqPanel.seqCanvas
+            .getWrappedCanvasWidth(seqPanelWidth);
+
+    int hgap = av.charHeight;
+    if (av.scaleAboveWrapped)
+    {
+      hgap += av.charHeight;
+    }
+
+    int annotationHeight = 0;
+    if (av.showAnnotation)
+    {
+      annotationHeight = annotationPanel.adjustPanelHeight();
+    }
+
+    int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+            + annotationHeight;
+
+    int maxwidth = av.getAlignment().getWidth();
+    if (av.hasHiddenColumns())
+    {
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+    }
+
+    int height = ((maxwidth / chunkWidth) + 1) * cHeight;
+
+    return height;
+  }
+
+  /**
+   * close the panel - deregisters all listeners and nulls any references to
+   * alignment data.
+   */
+  public void closePanel()
+  {
+    PaintRefresher.RemoveComponent(seqPanel.seqCanvas);
+    PaintRefresher.RemoveComponent(idPanel.idCanvas);
+    PaintRefresher.RemoveComponent(this);
+    if (av != null)
+    {
+      jalview.structure.StructureSelectionManager ssm = av
+              .getStructureSelectionManager();
+      ssm.removeStructureViewerListener(seqPanel, null);
+      ssm.removeSelectionListener(seqPanel);
+      av.setAlignment(null);
+      av = null;
+    }
+    else
+    {
+      if (Cache.log.isDebugEnabled())
+      {
+        Cache.log.warn("Closing alignment panel which is already closed.");
+      }
+    }
+  }
+
+  /**
+   * hides or shows dynamic annotation rows based on groups and av state flags
+   */
+  public void updateAnnotation()
+  {
+    updateAnnotation(false, false);
+  }
+
+  public void updateAnnotation(boolean applyGlobalSettings)
+  {
+    updateAnnotation(applyGlobalSettings, false);
+  }
+
+  public void updateAnnotation(boolean applyGlobalSettings,
+          boolean preserveNewGroupSettings)
+  {
+    av.updateGroupAnnotationSettings(applyGlobalSettings,
+            preserveNewGroupSettings);
+    adjustAnnotationHeight();
+  }
+
+  @Override
+  public AlignmentI getAlignment()
+  {
+    return av.getAlignment();
+  }
+
+  /**
+   * get the name for this view
+   * 
+   * @return
+   */
+  public String getViewName()
+  {
+    return av.viewName;
+  }
+
+  /**
+   * Make/Unmake this alignment panel the current input focus
+   * 
+   * @param b
+   */
+  public void setSelected(boolean b)
+  {
+    try
+    {
+      alignFrame.setSelected(b);
+    } catch (Exception ex)
+    {
+    }
+    ;
+
+    if (b)
+    {
+      alignFrame.setDisplayedView(this);
+    }
+  }
+
+  @Override
+  public StructureSelectionManager getStructureSelectionManager()
+  {
+    return av.getStructureSelectionManager();
+  }
+
+  @Override
+  public void raiseOOMWarning(String string, OutOfMemoryError error)
+  {
+    new OOMWarning(string, error, this);
+  }
+
+  public FeatureRenderer cloneFeatureRenderer()
+  {
+
+    return new FeatureRenderer(this);
+  }
+
+  public void updateFeatureRenderer(FeatureRenderer fr)
+  {
+    fr.transferSettings(seqPanel.seqCanvas.getFeatureRenderer());
+  }
+
+  public void updateFeatureRendererFrom(FeatureRenderer fr)
+  {
+    if (seqPanel.seqCanvas.getFeatureRenderer() != null)
+    {
+      seqPanel.seqCanvas.getFeatureRenderer().transferSettings(fr);
+    }
+  }
+}