/*
 * 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.*;


/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class AlignmentPanel extends GAlignmentPanel
    implements AdjustmentListener, Printable
{
  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);

    annotationPanel.adjustPanelHeight();
    annotationSpaceFillerHolder.setPreferredSize(annotationPanel.
                                                 getPreferredSize());
    annotationScroller.setPreferredSize(annotationPanel.
                                        getPreferredSize());
    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;

        }
      }
    });
  }

  /**
   * 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();
  }

  /**
   * 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();
      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].getStatus() != null && features[f].getStatus().length()>0)
                      {
                        text.append(" (" + features[f].getStatus() + ")");
                      }
                    }
                  }

                }
              }
              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 chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(
        seqPanel.seqCanvas.getWidth());

    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");
      }
    }
  }
}