/*
 * 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.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;

  public AnnotationPanel(AlignmentPanel ap)
  {
    this.ap = ap;
    av = ap.av;
    this.setLayout(null);
    adjustPanelHeight();

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

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

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

  public void 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].isGraph)
        {
          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);
    ap.annotationScroller.setSize(getSize().width, height);

//  ap.annotationSpaceFillerHolder.setSize(d.width,annotationPanel.getSize().height);

    repaint();

  }

  public void addEditableColumn(int i)
  {
    if (activeRow == -1)
    {
      AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
      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 (row > -1 && res < aa[row].annotations.length && aa[row].annotations[res] != null)
    {
      StringBuffer text = new StringBuffer("Sequence position " + (res + 1) +
                                           "  " +
                                           aa[row].annotations[res].description);
      ap.alignFrame.statusBar.setText(text.toString());
    }
  }

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

  public void paint(Graphics g)
  {
    imgWidth = (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();
  }

  public void drawComponent(Graphics g, int startRes, int endRes)
  {
    g.setColor(Color.white);
    g.fillRect(0, 0, (endRes - startRes) * av.charWidth, 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);
      g.drawString("Alignment has no annotations", 20, 15);
      return;
    }

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

    int j, x = 0, y = 0;
    char[] lastSS = new char[aa.length];
    int[] lastSSX = new int[aa.length];
    int iconOffset = av.charHeight / 2;
    boolean validRes = false;
    //\u03B2 \u03B1

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

      if (row.isGraph)
      {
        // 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;
      }

      for (j = startRes; j < endRes; j++)
      {
        if (row.annotations.length <= j || row.annotations[j] == null)
        {
          validRes = false;
        }
        else
        {
          validRes = true;
        }

        x = (j - startRes) * av.charWidth;

        if (activeRow == i)
        {

          g.setColor(Color.red);

          if (activeRes != null)
          {
            for (int n = 0; n < activeRes.size(); n++)
            {
              int v = Integer.parseInt(activeRes.elementAt(n).toString());
              if (v == j)
              {
                g.fillRect( (j - startRes) * av.charWidth, y, av.charWidth,
                           row.height);
              }
            }
          }
        }

        if (validRes && row.annotations[j].displayCharacter.length() > 0)
        {
          int charOffset = (av.charWidth -
                            fm.charWidth(row.annotations[j].displayCharacter.
                                         charAt(0))) / 2;
          g.setColor(row.annotations[j].colour);
          if (j == 0)
          {
            if (row.annotations[0].secondaryStructure == 'H'
                || row.annotations[0].secondaryStructure == 'E')
            {
              g.drawString(row.annotations[j].displayCharacter, x,
                           y + iconOffset + 2);
            }
          }
          else if ( (row.annotations[j].secondaryStructure == 'H'
                     || row.annotations[j].secondaryStructure == 'E') &&
                   (row.annotations[j - 1] == null ||
                    row.annotations[j].secondaryStructure !=
                    row.annotations[j - 1].secondaryStructure))
          {

            g.drawString(row.annotations[j].displayCharacter, x + charOffset,
                         y + iconOffset + 2);
          }

          if (!row.hasIcons)
          {
            g.drawString(row.annotations[j].displayCharacter, x + charOffset,
                         y + iconOffset + 2);
          }
        }

        if (row.hasIcons)
        {
          if (!validRes || row.annotations[j].secondaryStructure != lastSS[i])
          {
            switch (lastSS[i])
            {
              case 'H':
                g.setColor(HELIX_COLOUR);
                g.fillRoundRect(lastSSX[i], y + 4 + iconOffset, x - lastSSX[i],
                                7, 8, 8);
                break;
              case 'E':
                g.setColor(SHEET_COLOUR);
                g.fillRect(lastSSX[i], y + 4 + iconOffset, x - lastSSX[i] - 4,
                           7);
                g.fillPolygon(new int[]
                              {x - 4, x - 4, x}
                              , new int[]
                              {y + iconOffset, y + 14 + iconOffset,
                              y + 8 + iconOffset}, 3);
                break;
              case 'C':
                break;
              default:
                g.setColor(Color.gray);
                g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);
                break;
            }

            if (validRes)
            {
              lastSS[i] = row.annotations[j].secondaryStructure;
            }
            else
            {
              lastSS[i] = ' ';
            }
            lastSSX[i] = x;
          }
        }

        if (validRes && row.isGraph)
        {
          g.setColor(new Color(0, 0, 180));
          int height = (int) ( (row.annotations[j].value / row.graphMax) *
                              GRAPH_HEIGHT);

          if (row.windowLength > 1)
          {
            int total = 0;
            for (int i2 = j - (row.windowLength / 2);
                 i2 < j + (row.windowLength / 2); i2++)
            {
              if (i2 < 0 || i2 >= av.alignment.getWidth())
              {
                continue;
              }

              total += row.annotations[i2].value;
            }

            total /= row.windowLength;
            height = (int) ( (total / row.graphMax) * GRAPH_HEIGHT);

          }
          g.setColor(row.annotations[j].colour);
          g.fillRect(x, y - height, av.charWidth, height);
        }

      }

      x += av.charWidth;

      if (row.hasIcons)
      {
        switch (lastSS[i])
        {
          case 'H':
            g.setColor(HELIX_COLOUR);
            g.fillRoundRect(lastSSX[i], y + 4 + iconOffset, x - lastSSX[i], 7,
                            8, 8);
            break;
          case 'E':
            g.setColor(SHEET_COLOUR);
            g.fillRect(lastSSX[i], y + 4 + iconOffset, x - lastSSX[i] - 4, 7);
            g.fillPolygon(new int[]
                          {x - 4, x - 4, x}
                          , new int[]
                          {y + iconOffset, y + 14 + iconOffset,
                          y + 7 + iconOffset}
                          , 3);
            break;
          case 'C':
            break;
          default:
            g.setColor(Color.gray);
            g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);
            break;

        }
      }

      if (row.isGraph && row.hasText)
      {
        y += av.charHeight;
      }
      if (!row.isGraph)
      {
        y += aa[i].height;
      }
    }
  }

  // used by overview window
  public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y)
  {
    g.setColor(Color.white);
    g.fillRect(0, 0, width, y);
    g.setColor(new Color(0, 0, 180));
    int x = 0;
    for (int j = 0; j < aa.annotations.length; j++)
    {
      g.setColor(new Color(0, 0, 180));
      int height = (int) ( (aa.annotations[j].value / aa.graphMax) *
                          GRAPH_HEIGHT);
      g.fillRect(x, y - height, av.charWidth, height);
      x += av.charWidth;
    }
  }
}