/*
 * 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 java.util.*;

import java.awt.*;
import java.awt.event.*;
import java.awt.image.*;
import javax.swing.*;

import jalview.datamodel.*;

public class AnnotationPanel
    extends JPanel implements MouseListener,
    MouseMotionListener, ActionListener, AdjustmentListener
{
  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();

  public static int GRAPH_HEIGHT = 40;
  AlignViewport av;
  AlignmentPanel ap;
  int activeRow = -1;
  ArrayList activeRes;
  BufferedImage image;
  Graphics2D gg;
  FontMetrics fm;
  int imgWidth = 0;
  boolean fastPaint = false;

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

    ap.annotationScroller.getVerticalScrollBar().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.setPreferredSize(new Dimension(1, height));
  }

  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 ArrayList();
      activeRes.add(String.valueOf(i));

      return;
    }

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

  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 < activeRes.size(); i++)
      {
        anot[Integer.parseInt(activeRes.get(i).toString())] = null;
        anot[Integer.parseInt(activeRes.get(i).toString())] = null;
      }
    }
    else if (evt.getActionCommand().equals(LABEL))
    {
      String label = JOptionPane.showInputDialog(this, "Enter Label ",
                                                 "Enter label",
                                                 JOptionPane.QUESTION_MESSAGE);

      if (label == null)
      {
        label = "";
      }

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

      for (int i = 0; i < activeRes.size(); i++)
      {
        int index = Integer.parseInt(activeRes.get(i).toString());

        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 < activeRes.size(); i++)
      {
        int index = Integer.parseInt(activeRes.get(i).toString());

        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)
      {
        label = "";
      }

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

      for (int i = 0; i < activeRes.size(); i++)
      {
        int index = Integer.parseInt(activeRes.get(i).toString());

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

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

    adjustPanelHeight();
    activeRes = null;
    repaint();

    return;
  }

  public void mousePressed(MouseEvent evt)
  {
    if (SwingUtilities.isRightMouseButton(evt))
    {
      if (activeRes == 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;
    }

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

    if (aa == null)
    {
      return;
    }

    int height = 0;
    activeRow = -1;

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

      if (evt.getY() < height)
      {
        if (!aa[i].editable)
        {
          activeRes = null;

          continue;
        }

        activeRow = i;

        break;
      }
    }

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

    if (evt.isControlDown() || evt.isAltDown())
    {
      addEditableColumn(res);
    }
    else if (evt.isShiftDown())
    {
      if (activeRes == null)
      {
        activeRes = new ArrayList();
      }
      else
      {
        int start = Integer.parseInt(activeRes.get(activeRes.size() -
            1).toString());
        int end = res;

        if (end < start)
        {
          int temp = end;
          end = start;
          start = temp;
        }

        for (int n = start; n <= end; n++)
        {
          addEditableColumn(n);
        }
      }
    }
    else
    {
      activeRes = new ArrayList();
      activeRes.add(String.valueOf(res));
    }

    repaint();
  }

  public void mouseReleased(MouseEvent evt)
  {
  }

  public void mouseEntered(MouseEvent evt)
  {
  }

  public void mouseExited(MouseEvent evt)
  {
  }

  public void mouseDragged(MouseEvent evt)
  {
  }

  public void mouseMoved(MouseEvent evt)
  {
    ToolTipManager.sharedInstance().registerComponent(this);

    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))
    {
      this.setToolTipText(aa[row].annotations[res].description);

      StringBuffer text = new StringBuffer("Sequence position " +
                                           (res + 1) + "  " +
                                           aa[row].annotations[res].description);
      ap.alignFrame.statusBar.setText(text.toString());
    }
  }

  public void mouseClicked(MouseEvent evt)
  {
  }

  public void paintComponent(Graphics g)
  {
    g.setColor(Color.white);
    g.fillRect(0, 0, getWidth(), getHeight());

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

      return;
    }

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

    image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
                              BufferedImage.TYPE_INT_RGB);
    gg = (Graphics2D) image.getGraphics();
    gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
                        RenderingHints.VALUE_ANTIALIAS_ON);

    gg.setFont(av.getFont());
    fm = gg.getFontMetrics();

    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, 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();
  }

  public void drawComponent(Graphics2D g, int startRes, int endRes)
  {
    g.setColor(Color.white);
    g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());

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

      return;
    }

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

    int j;
    int x = 0;
    int 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.get(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,
                         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;
    }
  }
}