/*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2006 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 java.awt.*;
import java.awt.event.*;
import java.awt.image.*;

import javax.swing.*;


/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class AnnotationPanel extends JPanel implements MouseListener,
    MouseMotionListener, ActionListener, AdjustmentListener
{
    final String HELIX = "Helix";
    final String SHEET = "Sheet";
    final String LABEL = "Label";
    final String REMOVE = "Remove Annotation";
    final String COLOUR = "Colour";
    final Color HELIX_COLOUR = Color.red.darker();
    final Color SHEET_COLOUR = Color.green.darker().darker();

    /** DOCUMENT ME!! */
    AlignViewport av;
    AlignmentPanel ap;
    int activeRow = -1;
    BufferedImage image;
    BufferedImage fadedImage;
    Graphics2D gg;
    FontMetrics fm;
    int imgWidth = 0;
    boolean fastPaint = false;

    //Used For mouse Dragging and resizing graphs
    int graphStretch = -1;
    int graphStretchY = -1;
    int min; //used by mouseDragged to see if user
    int max; //used by mouseDragged to see if user
    boolean mouseDragging = false;

    boolean MAC = false;

    /**
     * Creates a new AnnotationPanel object.
     *
     * @param ap DOCUMENT ME!
     */
    public AnnotationPanel(AlignmentPanel ap)
    {

    if(System.getProperty("os.name").startsWith("Mac"))
      MAC = true;

        ToolTipManager.sharedInstance().registerComponent(this);
        ToolTipManager.sharedInstance().setInitialDelay(0);
        ToolTipManager.sharedInstance().setDismissDelay(10000);
        this.ap = ap;
        av = ap.av;
        this.setLayout(null);
        addMouseListener(this);
        addMouseMotionListener(this);
        ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);
    }

    public AnnotationPanel(AlignViewport av)
    {
      this.av = av;
    }


    /**
     * DOCUMENT ME!
     *
     * @param evt DOCUMENT ME!
     */
    public void adjustmentValueChanged(AdjustmentEvent evt)
    {
        ap.alabels.setScrollOffset(-evt.getValue());
    }

    /**
     * DOCUMENT ME!
     */
    public int adjustPanelHeight()
    {
        // setHeight of panels
        AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
        int height = 0;

        if (aa != null)
        {
            for (int i = 0; i < aa.length; i++)
            {
                if (!aa[i].visible)
                {
                    continue;
                }

                aa[i].height = 0;

                if (aa[i].hasText)
                {
                    aa[i].height += av.charHeight;
                }

                if (aa[i].hasIcons)
                {
                    aa[i].height += 16;
                }

                if (aa[i].graph>0)
                {
                    aa[i].height += aa[i].graphHeight;
                }

                if (aa[i].height == 0)
                {
                    aa[i].height = 20;
                }

                height += aa[i].height;
            }
        }
        else
        {
            height = 20;
        }

        this.setPreferredSize(new Dimension(1, height));

        return height;
    }



    /**
     * DOCUMENT ME!
     *
     * @param evt DOCUMENT ME!
     */
    public void actionPerformed(ActionEvent evt)
    {
        AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
        Annotation[] anot = aa[activeRow].annotations;

        if (evt.getActionCommand().equals(REMOVE))
        {
            for (int i = 0; i < av.getColumnSelection().size(); i++)
            {
                anot[av.getColumnSelection().columnAt(i)] = null;
            }
        }
        else if (evt.getActionCommand().equals(LABEL))
        {
            String label = JOptionPane.showInputDialog(this, "Enter Label ",
                    "Enter label", JOptionPane.QUESTION_MESSAGE);

            if (label == null)
            {
                return;
            }

            if ((label.length() > 0) && !aa[activeRow].hasText)
            {
                aa[activeRow].hasText = true;
            }

            for (int i = 0; i < av.getColumnSelection().size(); i++)
            {
                int index = av.getColumnSelection().columnAt(i);

                if (anot[index] == null)
                {
                    anot[index] = new Annotation(label, "", ' ', 0);
                }

                anot[index].displayCharacter = label;
            }
        }
        else if (evt.getActionCommand().equals(COLOUR))
        {
            Color col = JColorChooser.showDialog(this,
                    "Choose foreground colour", Color.black);

            for (int i = 0; i < av.getColumnSelection().size(); i++)
            {
                int index = av.getColumnSelection().columnAt(i);

                if (anot[index] == null)
                {
                    anot[index] = new Annotation("", "", ' ', 0);
                }

                anot[index].colour = col;
            }
        }
        else // HELIX OR SHEET
        {
            char type = 0;
            String symbol = "\u03B1";

            if (evt.getActionCommand().equals(HELIX))
            {
                type = 'H';
            }
            else if (evt.getActionCommand().equals(SHEET))
            {
                type = 'E';
                symbol = "\u03B2";
            }

            if (!aa[activeRow].hasIcons)
            {
                aa[activeRow].hasIcons = true;
            }

            String label = JOptionPane.showInputDialog("Enter a label for the structure?",
                    symbol);

            if (label == null)
            {
                return;
            }

            if ((label.length() > 0) && !aa[activeRow].hasText)
            {
                aa[activeRow].hasText = true;
            }

            for (int i = 0; i < av.getColumnSelection().size(); i++)
            {
                int index = av.getColumnSelection().columnAt(i);

                if (anot[index] == null)
                {
                    anot[index] = new Annotation(label, "", type, 0);
                }

                anot[index].secondaryStructure = type;
                anot[index].displayCharacter = label;
            }
        }

        adjustPanelHeight();
        repaint();

        return;
    }

    /**
     * DOCUMENT ME!
     *
     * @param evt DOCUMENT ME!
     */
    public void mousePressed(MouseEvent evt)
    {


        AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
        if(aa==null)
          return;


        int height = 0;
        activeRow = -1;


        for (int i = 0; i < aa.length; i++)
        {
            if (aa[i].visible)
            {
              height += aa[i].height;
            }

            if (evt.getY() < height)
            {
                if (aa[i].editable)
                {
                    activeRow = i;
                }
                else if(aa[i].graph>0)
                {
                    //Stretch Graph
                    graphStretch = i;
                    graphStretchY = evt.getY();
                }

                break;
            }
        }


        if (SwingUtilities.isRightMouseButton(evt) && activeRow!=-1)
        {
            if (av.getColumnSelection() == null)
            {
                return;
            }

            JPopupMenu pop = new JPopupMenu("Structure type");
            JMenuItem item = new JMenuItem(HELIX);
            item.addActionListener(this);
            pop.add(item);
            item = new JMenuItem(SHEET);
            item.addActionListener(this);
            pop.add(item);
            item = new JMenuItem(LABEL);
            item.addActionListener(this);
            pop.add(item);
            item = new JMenuItem(COLOUR);
            item.addActionListener(this);
            pop.add(item);
            item = new JMenuItem(REMOVE);
            item.addActionListener(this);
            pop.add(item);
            pop.show(this, evt.getX(), evt.getY());

            return;
        }

        if (aa == null)
        {
            return;
        }

        int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();

        min = res;
        max = res;

        if (av.getColumnSelection().contains(res))
          av.getColumnSelection().removeElement(res);
        else
        {
            av.getColumnSelection().addElement(res);
            SequenceGroup sg = new SequenceGroup();

            for (int i = 0; i < av.alignment.getSequences().size(); i++)
            {
                sg.addSequence(av.alignment.getSequenceAt(i), false);
            }

            sg.setStartRes(res);
            sg.setEndRes(res);
            av.setSelectionGroup(sg);
        }

        ap.repaint();

    }

    /**
     * DOCUMENT ME!
     *
     * @param evt DOCUMENT ME!
     */
    public void mouseReleased(MouseEvent evt)
    {
      graphStretch = -1;
      graphStretchY = -1;
      mouseDragging = false;
    }

    /**
     * DOCUMENT ME!
     *
     * @param evt DOCUMENT ME!
     */
    public void mouseEntered(MouseEvent evt)
    {
      if(mouseDragging)
        ap.seqPanel.scrollCanvas(null);
    }

    /**
     * DOCUMENT ME!
     *
     * @param evt DOCUMENT ME!
     */
    public void mouseExited(MouseEvent evt)
    {
      if(mouseDragging)
        ap.seqPanel.scrollCanvas(evt);
    }


    /**
     * DOCUMENT ME!
     *
     * @param evt DOCUMENT ME!
     */
    public void mouseDragged(MouseEvent evt)
    {
      if(graphStretch>-1)
      {
        av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - evt.getY();
        if(av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight <0)
          av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;
        graphStretchY = evt.getY();
        adjustPanelHeight();
        ap.repaint();
      }
      else
      {
        mouseDragging = true;

        int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();

        SequenceGroup sg = av.getSelectionGroup();

        if (res < min)
        {
            min = res;
        }

        if (res > max)
        {
            max = res;
        }

        if (sg != null)
        {
            if (!av.getColumnSelection().contains(res))
            {
                av.getColumnSelection().addElement(res);
            }

            if (res > sg.getStartRes())
            {
                sg.setEndRes(res);
            }
            else if (res < sg.getStartRes())
            {
                sg.setStartRes(res);
            }

            for (int i = min; i <= max; i++)
            {
                if ((i < sg.getStartRes()) || (i > sg.getEndRes()))
                {
                    av.getColumnSelection().removeElement(i);
                }
                else
                {
                    av.getColumnSelection().addElement(i);
                }
            }

            ap.repaint();
        }

      }
    }

    /**
     * DOCUMENT ME!
     *
     * @param evt DOCUMENT ME!
     */
    public void mouseMoved(MouseEvent evt)
    {
        AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();

        if (aa == null)
        {
            return;
        }

        int row = -1;
        int height = 0;

        for (int i = 0; i < aa.length; i++)
        {
            if (aa[i].visible)
            {
                height += aa[i].height;
            }

            if (evt.getY() < height)
            {
                row = i;

                break;
            }
        }

        if(row==-1)
          return;

        int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();

        if(av.hasHiddenColumns)
          res = av.getColumnSelection().adjustForHiddenColumns(res);

        if ( aa[row].annotations!=null
             && row > -1
             && res < (int) aa[row].annotations.length)
        {
            if(aa[row].graphGroup>-1)
            {
              StringBuffer tip = new StringBuffer("<html>");
              for (int gg = 0; gg < aa.length; gg++)
              {
                if (aa[gg].graphGroup == aa[row].graphGroup && aa[gg].annotations[res]!=null)
                  tip.append(aa[gg].label+" "+aa[gg].annotations[res].description+"<br>" );
              }
              if(tip.length()!=6)
              {
                tip.setLength(tip.length() - 4);
                this.setToolTipText(tip.toString() + "</html>");
              }
            }
            else if(aa[row].annotations[res] != null)
              this.setToolTipText(aa[row].annotations[res].description);

            if(aa[row].annotations[res]!=null)
            {
              StringBuffer text = new StringBuffer("Sequence position " +
                                                   (res + 1) + "  " +
                                                   aa[row].annotations[res].description);

              ap.alignFrame.statusBar.setText(text.toString());
            }
        }
    }

    /**
     * DOCUMENT ME!
     *
     * @param evt DOCUMENT ME!
     */
    public void mouseClicked(MouseEvent evt)
    {
    }

    /**
     * DOCUMENT ME!
     *
     * @param g DOCUMENT ME!
     */
    public void paintComponent(Graphics g)
    {
      g.setColor(Color.white);
      g.fillRect(0, 0, getWidth(), getHeight());

      if(image!=null)
      {if (fastPaint
            || (getVisibleRect().width != g.getClipBounds().width)
            || (getVisibleRect().height != g.getClipBounds().height))
        {
          g.drawImage(image, 0, 0, this);
          fastPaint = false;
          return;
        }
      }
      imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;

      if (image == null || imgWidth != image.getWidth()
          || image.getHeight(this) != getHeight())
      {
        image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
                                  BufferedImage.TYPE_INT_RGB);
        gg = (Graphics2D) image.getGraphics();

        if(av.antiAlias)
        gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
                            RenderingHints.VALUE_ANTIALIAS_ON);

        gg.setFont(av.getFont());
        fm = gg.getFontMetrics();
        gg.setColor(Color.white);
        gg.fillRect(0, 0, imgWidth, image.getHeight());
      }


      drawComponent(gg, av.startRes, av.endRes + 1);
      g.drawImage(image, 0, 0, this);
    }

    /**
     * DOCUMENT ME!
     *
     * @param horizontal DOCUMENT ME!
     */
    public void fastPaint(int horizontal)
    {
        if ((horizontal == 0)
            || gg==null
            || av.alignment.getAlignmentAnnotation()==null
            || av.alignment.getAlignmentAnnotation().length < 1
            || av.updatingConsensus
            || av.updatingConservation)
        {
            repaint();
            return;
        }

        gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);

        int sr = av.startRes;
        int er = av.endRes + 1;
        int transX = 0;

        if (horizontal > 0) // scrollbar pulled right, image to the left
        {
            transX = (er - sr - horizontal) * av.charWidth;
            sr = er - horizontal;
        }
        else if (horizontal < 0)
        {
            er = sr - horizontal;
        }

        gg.translate(transX, 0);

        drawComponent(gg, sr, er);

        gg.translate(-transX, 0);

        fastPaint = true;

        repaint();

    }

    /**
     * DOCUMENT ME!
     *
     * @param g DOCUMENT ME!
     * @param startRes DOCUMENT ME!
     * @param endRes DOCUMENT ME!
     */
    public void drawComponent(Graphics g, int startRes, int endRes)
    {
      if(av.updatingConsensus || av.updatingConservation)
      {
        if(image==null)
         {
           return;
         }
        //We'll keep a record of the old image,
        //and draw a faded image until the calculation
        //has completed
        if(fadedImage==null
           || fadedImage.getWidth()!=imgWidth
        || fadedImage.getHeight()!=image.getHeight())
        {
          fadedImage = new BufferedImage(
              imgWidth, image.getHeight(),
              BufferedImage.TYPE_INT_RGB);

          Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();

          fadedG.setColor(Color.white);
        fadedG.fillRect(0, 0, imgWidth, image.getHeight());

          fadedG.setComposite(
              AlphaComposite.getInstance(
                  AlphaComposite.SRC_OVER, .3f));
          fadedG.drawImage(image, 0, 0, this);

        }

      }
      else
        fadedImage = null;


      g.setColor(Color.white);
      g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());

      g.setFont(av.getFont());
      if (fm == null)
        fm = g.getFontMetrics();




        if ( (av.alignment.getAlignmentAnnotation() == null) ||
                (av.alignment.getAlignmentAnnotation().length < 1))
        {
            g.setColor(Color.white);
            g.fillRect(0, 0, getWidth(), getHeight());
            g.setColor(Color.black);
            if(av.validCharWidth)
              g.drawString("Alignment has no annotations", 20, 15);

            return;
        }


        AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();

        int x = 0, y = 0;
        int column=0;
        char lastSS;
        int lastSSX;
        int iconOffset = av.charHeight / 2;
        boolean validRes = false;

        boolean [] graphGroupDrawn = new boolean[aa.length];


        //\u03B2 \u03B1
        for (int i = 0; i < aa.length; i++)
        {
            AlignmentAnnotation row = aa[i];

            if (!row.visible)
            {
                continue;
            }


            lastSS = ' ';
            lastSSX = 0;

            if (row.graph>0)
            {
                if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] )
                  continue;

                // this is so that we draw the characters below the graph
                y += row.height;

                if (row.hasText)
                {
                    y -= av.charHeight;
                }
            }

            if (av.updatingConsensus && aa[i].label.equals("Consensus"))
            {
              y += av.charHeight;

              g.drawImage(fadedImage,
              0,y-row.height,imgWidth, y,
              0,y-row.height,imgWidth, y, this);
              g.setColor(Color.black);
             // g.drawString("Calculating Consensus....",20, y-row.height/2);

              continue;
            }
            else if (av.updatingConservation && aa[i].label.equals("Conservation"))
            {

              y += av.charHeight;
              g.drawImage(fadedImage,
                          0, y - row.height, imgWidth, y,
                          0, y - row.height, imgWidth, y, this);

              g.setColor(Color.black);
            //  g.drawString("Calculating Conservation.....",20, y-row.height/2);

              continue;
            }
            else if (av.updatingConservation && aa[i].label.equals("Quality"))
            {

              y += av.charHeight;
              g.drawImage(fadedImage,
                          0, y - row.height, imgWidth, y,
                          0, y - row.height, imgWidth, y, this);
              g.setColor(Color.black);
             /// g.drawString("Calculating Quality....",20, y-row.height/2);

              continue;
            }


            if (row.hasText)
            {
                iconOffset = av.charHeight / 2 + 4;
            }
            else
            {
                iconOffset = 0;
            }

            x = 0;
            while (x < endRes-startRes)
            {
              if (av.hasHiddenColumns)
              {
                column = av.getColumnSelection().adjustForHiddenColumns(startRes+x);
                if (column > row.annotations.length-1)
                {
                  break;
                }
              }
              else
                column = startRes+x;


                if ((row.annotations.length <= column) ||
                        (row.annotations[column] == null))
                {
                    validRes = false;
                }
                else
                {
                    validRes = true;
                }


                if (activeRow == i)
                {
                    g.setColor(Color.red);

                    if (av.getColumnSelection() != null)
                    {
                        for (int n = 0; n < av.getColumnSelection().size(); n++)
                        {
                            int v = av.getColumnSelection().columnAt(n);

                            if (v == column)
                            {
                                g.fillRect(x * av.charWidth, y,
                                    av.charWidth, av.charHeight);
                            }
                        }
                    }
                }

                if (av.validCharWidth && validRes &&
                        (row.annotations[column].displayCharacter.length() > 0))
                {

                    int charOffset = (av.charWidth -
                        fm.charWidth(row.annotations[column].displayCharacter.charAt(
                                0))) / 2;
                    g.setColor(row.annotations[column].colour);

                    if (column == 0 || row.graph>0)
                    {
                        g.drawString(row.annotations[column].displayCharacter,
                                     (x*av.charWidth)+charOffset,
                            y + iconOffset );
                    }
                    else if (
                        row.annotations[column - 1] == null
                        ||(!row.annotations[column].displayCharacter.equals(
                            row.annotations[column - 1].displayCharacter)
                        ||
                  (row.annotations[column].displayCharacter.length() <2 &&
                   row.annotations[column].secondaryStructure==' ')))
                    {
                        g.drawString(row.annotations[column].displayCharacter,
                                     x*av.charWidth+charOffset,
                                     y + iconOffset );
                    }
                }

                if (row.hasIcons)
                {
                    if (!validRes ||
                            (row.annotations[column].secondaryStructure != lastSS))
                    {
                        switch (lastSS)
                        {
                        case 'H':
                          g.setColor(HELIX_COLOUR);
                          if (MAC)
                          {
                            //Off by 1 offset when drawing rects and ovals
                            //to offscreen image on the MAC
                            g.fillRoundRect(lastSSX, y + 4 + iconOffset,
                                            (x*av.charWidth) - lastSSX, 7, 8, 8);
                            break;
                          }

                          int sCol = (lastSSX / av.charWidth) + startRes;
                          int x1 = lastSSX;
                          int x2 = (x*av.charWidth);

                         if(sCol==0 ||
                            row.annotations[sCol-1]==null ||
                            row.annotations[sCol-1].secondaryStructure!='H')
                         {
                           g.fillArc(lastSSX, y+4+iconOffset, av.charWidth, 8, 90,180) ;
                           x1 += av.charWidth/2;
                         }

                          if(row.annotations[column]==null ||
                             row.annotations[column].secondaryStructure!='H')
                          {
                            g.fillArc((x*av.charWidth)-av.charWidth,
                                      y+4+iconOffset, av.charWidth, 8, 270,180);
                            x2 -= av.charWidth/2;
                          }

                          g.fillRect(x1, y+4+iconOffset, x2-x1, 8);
                              break;

                        case 'E':
                            g.setColor(SHEET_COLOUR);
                            g.fillRect(lastSSX, y + 4 + iconOffset,
                                (x*av.charWidth) - lastSSX - 4, 7);
                            g.fillPolygon(new int[] { (x*av.charWidth) - 4,
                                          (x*av.charWidth) - 4,
                                          (x*av.charWidth) },
                                new int[]
                                {
                                    y + iconOffset, y + 14 + iconOffset,
                                    y + 8 + iconOffset
                                }, 3);

                            break;


                        default:
                            g.setColor(Color.gray);
                            g.fillRect(lastSSX, y + 6 + iconOffset,
                                (x*av.charWidth) - lastSSX, 2);

                            break;
                        }

                        if (validRes)
                        {
                            lastSS = row.annotations[column].secondaryStructure;
                        }
                        else
                        {
                            lastSS = ' ';
                        }

                        lastSSX = (x*av.charWidth);
                    }
                }


            column++;
            x++;
            }

            if(column>=row.annotations.length)
                column = row.annotations.length-1;

          //  x ++;

            if (row.hasIcons)
            {
              switch (lastSS)
              {
                case 'H':
                  g.setColor(HELIX_COLOUR);
                  if (MAC)
                  {
                    //Off by 1 offset when drawing rects and ovals
                    //to offscreen image on the MAC
                    g.fillRoundRect(lastSSX, y + 4 + iconOffset,
                                    (x*av.charWidth) - lastSSX, 7, 8, 8);
                    break;
                  }

                  int sCol = (lastSSX / av.charWidth) + startRes;
                  int x1 = lastSSX;
                  int x2 = (x*av.charWidth);

                  if (sCol == 0 ||
                      row.annotations[sCol - 1] == null ||
                      row.annotations[sCol - 1].secondaryStructure != 'H')
                  {
                    g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, 180);
                    x1 += av.charWidth / 2;
                  }

                  if (row.annotations[column] == null ||
                      row.annotations[column].secondaryStructure != 'H')
                  {
                    g.fillArc((x*av.charWidth) - av.charWidth,
                              y + 4 + iconOffset, av.charWidth, 8, 270,
                              180);
                    x2 -= av.charWidth / 2;
                  }

                  g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);

                  break;

                case 'E':
                  g.setColor(SHEET_COLOUR);

                  if (row.annotations[endRes] == null
                      || row.annotations[endRes].secondaryStructure != 'E')
                  {
                    g.fillRect(lastSSX, y + 4 + iconOffset,
                               (x*av.charWidth) - lastSSX - 4, 7);
                    g.fillPolygon(new int[]
                                  {(x*av.charWidth) - 4,
                                  (x*av.charWidth) - 4,
                                 (x*av.charWidth)},
                                  new int[]
                                  {
                                  y + iconOffset, y + 14 + iconOffset,
                                  y + 7 + iconOffset
                    }, 3);
                  }
                  else
                   {
                     g.fillRect(lastSSX, y + 4 + iconOffset,
                                (x+1) * av.charWidth - lastSSX, 7);
                   }
                  break;

                default:
                  g.setColor(Color.gray);
                  if(!av.wrapAlignment || endRes==av.endRes)
                  g.fillRect(lastSSX, y + 6 + iconOffset,
                             (x*av.charWidth) - lastSSX, 2);

                  break;
              }
          }

            if (row.graph>0 && row.graphHeight>0)
            {
                if(row.graph == AlignmentAnnotation.LINE_GRAPH )
                {
                  if(row.graphGroup>-1 && !graphGroupDrawn[row.graphGroup])
                   {
                     float groupmax=-999999, groupmin=9999999;
                     for(int gg=0; gg<aa.length; gg++)
                     {
                       if(aa[gg].graphGroup!=row.graphGroup)
                         continue;

                       if(aa[gg]!=row)
                         aa[gg].visible = false;

                       if(aa[gg].graphMax>groupmax)
                         groupmax = aa[gg].graphMax;
                       if(aa[gg].graphMin<groupmin)
                         groupmin = aa[gg].graphMin;
                     }

                     for (int gg = 0; gg < aa.length; gg++)
                     {
                       if (aa[gg].graphGroup == row.graphGroup)
                       {
                         drawLineGraph(g, aa[gg], startRes, endRes, y,
                                       groupmin, groupmax,
                                       row.graphHeight);
                       }
                     }

                     graphGroupDrawn[ row.graphGroup ] = true;
                   }
                   else
                     drawLineGraph(g, row, startRes, endRes,
                                   y, row.graphMin, row.graphMax, row.graphHeight  );
                }
                else if(row.graph == AlignmentAnnotation.BAR_GRAPH )
                   drawBarGraph(g, row, startRes, endRes,
                                row.graphMin, row.graphMax, y);
            }

            if (row.graph>0 && row.hasText)
            {
                y += av.charHeight;
            }

            if (row.graph==0)
            {
                y += aa[i].height;
            }
        }
    }

    public void drawLineGraph(Graphics g, AlignmentAnnotation aa,
                              int sRes, int eRes,
                              int y,
                              float min, float max,
                              int graphHeight)
    {
      if(sRes>aa.annotations.length)
        return;


      int x = 0;

      //Adjustment for fastpaint to left
      if(eRes<av.endRes)
        eRes++;

      eRes = Math.min(eRes, aa.annotations.length);

      if(sRes==0)
      {
        x++;
      }

      int y1=y, y2=y;
      float range = max - min;

      ////Draw origin
      if(min<0)
        y2 = y - (int)((0-min / range)*graphHeight);

      g.setColor(Color.gray);
      g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);

      eRes = Math.min(eRes, aa.annotations.length);

      int column;
      int aaMax = aa.annotations.length-1;

      while( x < eRes - sRes )
      {
        column = sRes + x;
        if(av.hasHiddenColumns)
        {
          column = av.getColumnSelection().adjustForHiddenColumns(column);
        }

        if (column > aaMax)
        {
          break;
        }

        if(aa.annotations[column]==null || aa.annotations[column-1]==null)
        {
          x++;
          continue;
        }


          g.setColor(aa.annotations[column].colour);
          y1 = y - (int) (((aa.annotations[column-1].value-min) / range) * graphHeight);
          y2 = y - (int) (((aa.annotations[column].value-min) / range) * graphHeight);

          g.drawLine(x*av.charWidth-av.charWidth/2, y1, x*av.charWidth+av.charWidth/2, y2);
          x ++;
       }

       if(aa.threshold!=null)
       {
           g.setColor(aa.threshold.colour);
           Graphics2D g2 = (Graphics2D)g;
           g2.setStroke(new BasicStroke(1,
                                         BasicStroke.CAP_SQUARE,
                                         BasicStroke.JOIN_ROUND, 3f,
                                         new float[] { 5f, 3f }, 0f));

           y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);
           g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);
           g2.setStroke(new BasicStroke());
      }
    }

    public void drawBarGraph(Graphics g, AlignmentAnnotation aa,
                             int sRes, int eRes,
                             float min, float max,
                             int y)
    {
      if(sRes>aa.annotations.length)
        return;

      eRes = Math.min(eRes, aa.annotations.length);

      int x=0, y1=y, y2=y;

      float range = max - min;

      if(min<0)
        y2 = y - (int)((0-min / (range))*aa.graphHeight);

      g.setColor(Color.gray);

      g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);

      int column;
      int aaMax = aa.annotations.length-1;

      while( x < eRes-sRes )
      {
        column = sRes + x;
        if(av.hasHiddenColumns)
        {
          column = av.getColumnSelection().adjustForHiddenColumns(column);
        }

        if(column > aaMax)
        {
            break;
        }

        if (aa.annotations[column] == null)
        {
          x ++;
          continue;
        }

          g.setColor(aa.annotations[column].colour);
          y1 = y - (int) (((aa.annotations[column].value-min) / (range)) * aa.graphHeight);

          if(y1-y2>0)
            g.fillRect(x*av.charWidth, y2, av.charWidth, y1-y2 );
          else
            g.fillRect(x*av.charWidth, y1, av.charWidth, y2-y1 );

          x ++ ;

      }
      if(aa.threshold!=null)
      {
          g.setColor(aa.threshold.colour);
          Graphics2D g2 = (Graphics2D)g;
          g2.setStroke(new BasicStroke(1,
                                        BasicStroke.CAP_SQUARE,
                                        BasicStroke.JOIN_ROUND, 3f,
                                        new float[] { 5f, 3f }, 0f));

          y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);
          g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);
          g2.setStroke(new BasicStroke());
      }
    }

    // used by overview window
    public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)
    {
      eRes = Math.min(eRes, aa.annotations.length);
      g.setColor(Color.white);
      g.fillRect(0, 0, width, y);
      g.setColor(new Color(0, 0, 180));

      int x = 0, height;

      for (int j = sRes; j < eRes; j++)
      {
        if (aa.annotations[j] != null)
        {
          g.setColor(aa.annotations[j].colour);

          height = (int) ( (aa.annotations[j].value / aa.graphMax) * y);
          if (height > y)
            height = y;

          g.fillRect(x, y - height, av.charWidth, height);
        }
          x += av.charWidth;
      }
    }

}