/*
 * 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.appletgui;

import java.util.*;

import java.awt.*;
import java.awt.event.*;

import jalview.datamodel.*;

public class AnnotationPanel
    extends Panel implements AdjustmentListener
{
  AlignViewport av;
  AlignmentPanel ap;
  int activeRow = -1;

  Vector activeRes;
  static String HELIX = "Helix";
  static String SHEET = "Sheet";
  static String LABEL = "Label";
  static String REMOVE = "Remove Annotation";
  static String COLOUR = "Colour";
  static Color HELIX_COLOUR = Color.red.darker();
  static Color SHEET_COLOUR = Color.green.darker().darker();

  Image image;
  Graphics gg;
  FontMetrics fm;
  int imgWidth = 0;

  boolean fastPaint = false;

  public static int GRAPH_HEIGHT = 40;

  boolean MAC = false;

  public AnnotationPanel(AlignmentPanel ap)
  {
    if (System.getProperty("os.name").startsWith("Mac"))
      MAC = true;

    this.ap = ap;
    av = ap.av;
    setLayout(null);
    adjustPanelHeight();

    addMouseMotionListener(new MouseMotionAdapter()
    {
      public void mouseMoved(MouseEvent evt)
      {
        doMouseMoved(evt);
      }
    });

    // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );
  }


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


  public void adjustmentValueChanged(AdjustmentEvent evt)
  {
    ap.alabels.setScrollOffset( -evt.getValue());
  }

  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 += GRAPH_HEIGHT;
        }

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

    this.setSize(getSize().width, height);

    repaint();

    return height;

  }

  public void addEditableColumn(int i)
  {
    if (activeRow == -1)
    {
      AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
      if(aa ==null)
        return;

      for (int j = 0; j < aa.length; j++)
      {
        if (aa[j].editable)
        {
          activeRow = j;
          break;
        }
      }
    }

    if (activeRes == null)
    {
      activeRes = new Vector();
      activeRes.addElement(String.valueOf(i));
      return;
    }

    activeRes.addElement(String.valueOf(i));
  }

  public void doMouseMoved(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;
      }
    }

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

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

        if (row > -1 && res < aa[row].annotations.length && aa[row].annotations[res] != null)
        {
          StringBuffer text = new StringBuffer("Sequence position " + (res + 1));
          if (aa[row].annotations[res].description != null)
            text.append("  " + aa[row].annotations[res].description);
          ap.alignFrame.statusBar.setText(text.toString());
        }
  }

  public void update(Graphics g)
  {
    paint(g);
  }

  public void paint(Graphics g)
  {

    imgWidth = getSize().width;
        //(av.endRes - av.startRes + 1) * av.charWidth;

    if (image == null || imgWidth != image.getWidth(this))
    {
      image = createImage(imgWidth, ap.annotationPanel.getSize().height);
      gg = image.getGraphics();
      gg.setFont(av.getFont());
      fm = gg.getFontMetrics();
      fastPaint = false;
    }

    if (fastPaint)
    {
      g.drawImage(image, 0, 0, this);
      fastPaint = false;
      return;
    }

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

  public void fastPaint(int horizontal)
  {
    if (horizontal == 0
        || av.alignment.getAlignmentAnnotation() == null
        || av.alignment.getAlignmentAnnotation().length < 1
        )
    {
      repaint();
      return;
    }

    gg.copyArea(0, 0, imgWidth, getSize().height, -horizontal * av.charWidth, 0);
    int sr = av.startRes, er = av.endRes + 1, 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)
  {
    g.setFont(av.getFont());

    if (fm == null)
      fm = g.getFontMetrics();


      g.setColor(Color.white);
      g.fillRect(0, 0, getSize().width, getSize().height);

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

          return;
      }

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

      int x = 0;
      int 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 (row.hasText)
          {
              iconOffset = av.charHeight / 2;
          }
          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 (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 + 3);
                }
                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 + 3);
                    }
              }

              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 * 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)
          {
              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)
    {
      sRes++;
      x+=av.charWidth;
    }

    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)*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);

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

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

  // used by overview window
  public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)
  {
      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++)
      {
          g.setColor(aa.annotations[j].colour);

          height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);
          if(height>y)
              height = y;
          g.fillRect(x, y - height, av.charWidth, height);
          x += av.charWidth;
      }
    }
}