/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview 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 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.appletgui;

import jalview.datamodel.AlignmentI;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import jalview.viewmodel.AlignmentViewport;

import java.awt.Color;
import java.awt.FontMetrics;
import java.awt.Graphics;
import java.awt.Image;
import awt2swing.Panel;

public class SeqCanvas extends Panel
{
  FeatureRenderer fr;

  SequenceRenderer sr;

  Image img;

  Graphics gg;

  int imgWidth;

  int imgHeight;

  AlignViewport av;

  SearchResults searchResults = null;

  boolean fastPaint = false;

  int cursorX = 0;

  int cursorY = 0;

  public SeqCanvas(AlignViewport av)
  {
    this.av = av;
    fr = new FeatureRenderer(av);
    sr = new SequenceRenderer(av);
    PaintRefresher.Register(this, av.getSequenceSetId());
    updateViewport();
  }

  int avcharHeight = 0, avcharWidth = 0;

  private void updateViewport()
  {
    avcharHeight = av.getCharHeight();
    avcharWidth = av.getCharWidth();
  }

  public AlignmentViewport getViewport()
  {
    return av;
  }

  public FeatureRenderer getFeatureRenderer()
  {
    return fr;
  }

  public SequenceRenderer getSequenceRenderer()
  {
    return sr;
  }

  private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
  {
    int scalestartx = startx - startx % 10 + 10;

    g.setColor(Color.black);

    // NORTH SCALE
    for (int i = scalestartx; i < endx; i += 10)
    {
      int value = i;
      if (av.hasHiddenColumns())
      {
        value = av.getColumnSelection().adjustForHiddenColumns(value);
      }

      awt2swing.Util.drawString(g, String.valueOf(value), (i - startx - 1) * avcharWidth,
              ypos - (avcharHeight / 2));

      g.drawLine(((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
              (ypos + 2) - (avcharHeight / 2),
              ((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
              ypos - 2);
    }
  }

  private void drawWestScale(Graphics g, int startx, int endx, int ypos)
  {
    FontMetrics fm = getFontMetrics(av.getFont());
    ypos += avcharHeight;
    if (av.hasHiddenColumns())
    {
      startx = av.getColumnSelection().adjustForHiddenColumns(startx);
      endx = av.getColumnSelection().adjustForHiddenColumns(endx);
    }

    int maxwidth = av.getAlignment().getWidth();
    if (av.hasHiddenColumns())
    {
      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
    }

    // WEST SCALE
    for (int i = 0; i < av.getAlignment().getHeight(); i++)
    {
      SequenceI seq = av.getAlignment().getSequenceAt(i);
      int index = startx;
      int value = -1;

      while (index < endx)
      {
        if (Comparison.isGap(seq.getCharAt(index)))
        {
          index++;

          continue;
        }

        value = av.getAlignment().getSequenceAt(i).findPosition(index);

        break;
      }

      if (value != -1)
      {
        int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
                - avcharWidth / 2;
        awt2swing.Util.drawString(g, value + "", x, (ypos + (i * avcharHeight))
                - (avcharHeight / 5));
      }
    }
  }

  private void drawEastScale(Graphics g, int startx, int endx, int ypos)
  {
    ypos += avcharHeight;

    if (av.hasHiddenColumns())
    {
      endx = av.getColumnSelection().adjustForHiddenColumns(endx);
    }

    SequenceI seq;
    // EAST SCALE
    for (int i = 0; i < av.getAlignment().getHeight(); i++)
    {
      seq = av.getAlignment().getSequenceAt(i);
      int index = endx;
      int value = -1;

      while (index > startx)
      {
        if (Comparison.isGap(seq.getCharAt(index)))
        {
          index--;

          continue;
        }

        value = seq.findPosition(index);

        break;
      }

      if (value != -1)
      {
        awt2swing.Util.drawString(g, String.valueOf(value), 0, (ypos + (i * avcharHeight))
                - (avcharHeight / 5));
      }
    }
  }

  int lastsr = 0;

  void fastPaint(int horizontal, int vertical)
  {
    if (fastPaint || gg == null)
    {
      return;
    }

    updateViewport();

    // Its possible on certain browsers that the call to fastpaint
    // is faster than it can paint, so this check here catches
    // this possibility
    if (lastsr + horizontal != av.startRes)
    {
      horizontal = av.startRes - lastsr;
    }

    lastsr = av.startRes;

    fastPaint = true;
    gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight, imgWidth
            - horizontal * avcharWidth,
            imgHeight - vertical * avcharHeight, -horizontal * avcharWidth,
            -vertical * avcharHeight);

    int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0;

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

    else if (vertical > 0) // scroll down
    {
      ss = es - vertical;
      if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
      {
        ss = av.startSeq;
      }
      else
      {
        transY = imgHeight - vertical * avcharHeight;
      }
    }
    else if (vertical < 0)
    {
      es = ss - vertical;
      if (es > av.endSeq)
      {
        es = av.endSeq;
      }
    }

    gg.translate(transX, transY);

    drawPanel(gg, sr, er, ss, es, 0);
    gg.translate(-transX, -transY);

    repaint();

  }

  /**
   * Definitions of startx and endx (hopefully): SMJS This is what I'm working
   * towards! startx is the first residue (starting at 0) to display. endx is
   * the last residue to display (starting at 0). starty is the first sequence
   * to display (starting at 0). endy is the last sequence to display (starting
   * at 0). NOTE 1: The av limits are set in setFont in this class and in the
   * adjustment listener in SeqPanel when the scrollbars move.
   */

  @Override
  public void paintComponent(Graphics g)
  {
    if (img != null
            && (fastPaint || (getSize().width != g.getClipBounds().width) || (getSize().height != g
                    .getClipBounds().height)))
    {
      g.drawImage(img, 0, 0, this);
      fastPaint = false;
      return;
    }

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

    updateViewport();
    // this draws the whole of the alignment
    imgWidth = this.getSize().width;
    imgHeight = this.getSize().height;

    imgWidth -= imgWidth % avcharWidth;
    imgHeight -= imgHeight % avcharHeight;

    if (imgWidth < 1 || imgHeight < 1)
    {
      return;
    }

    if (img == null || imgWidth != img.getWidth(this)
            || imgHeight != img.getHeight(this))
    {
      img = createImage(imgWidth, imgHeight);
      gg = img.getGraphics();
      gg.setFont(av.getFont());
    }

    gg.setColor(Color.white);
    gg.fillRect(0, 0, imgWidth, imgHeight);

    if (av.getWrapAlignment())
    {
      drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
    }
    else
    {
      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
    }

    g.drawImage(img, 0, 0, this);

  }

  int LABEL_WEST, LABEL_EAST;

  public int getWrappedCanvasWidth(int cwidth)
  {
    cwidth -= cwidth % av.getCharWidth();

    FontMetrics fm = getFontMetrics(av.getFont());

    LABEL_EAST = 0;
    LABEL_WEST = 0;

    if (av.getScaleRightWrapped())
    {
      LABEL_EAST = fm.stringWidth(getMask());
    }

    if (av.getScaleLeftWrapped())
    {
      LABEL_WEST = fm.stringWidth(getMask());
    }

    return (cwidth - LABEL_EAST - LABEL_WEST) / av.getCharWidth();
  }

  /**
   * Generates a string of zeroes.
   * 
   * @return String
   */
  String getMask()
  {
    String mask = "0";
    int maxWidth = 0;
    int tmp;
    AlignmentI alignment = av.getAlignment();
    for (int i = 0; i < alignment.getHeight(); i++)
    {
      tmp = alignment.getSequenceAt(i).getEnd();
      if (tmp > maxWidth)
      {
        maxWidth = tmp;
      }
    }

    for (int i = maxWidth; i > 0; i /= 10)
    {
      mask += "0";
    }
    return mask;
  }

  private void drawWrappedPanel(Graphics g, int canvasWidth,
          int canvasHeight, int startRes)
  {
    AlignmentI al = av.getAlignment();

    FontMetrics fm = getFontMetrics(av.getFont());

    if (av.getScaleRightWrapped())
    {
      LABEL_EAST = fm.stringWidth(getMask());
    }

    if (av.getScaleLeftWrapped())
    {
      LABEL_WEST = fm.stringWidth(getMask());
    }

    int hgap = avcharHeight;
    if (av.getScaleAboveWrapped())
    {
      hgap += avcharHeight;
    }

    int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / avcharWidth;
    int cHeight = av.getAlignment().getHeight() * avcharHeight;

    av.setWrappedWidth(cWidth);

    av.endRes = av.startRes + cWidth;

    int endx;
    int ypos = hgap;

    int maxwidth = av.getAlignment().getWidth() - 1;

    if (av.hasHiddenColumns())
    {
      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
    }

    while ((ypos <= canvasHeight) && (startRes < maxwidth))
    {
      endx = startRes + cWidth - 1;

      if (endx > maxwidth)
      {
        endx = maxwidth;
      }

      g.setColor(Color.black);

      if (av.getScaleLeftWrapped())
      {
        drawWestScale(g, startRes, endx, ypos);
      }

      if (av.getScaleRightWrapped())
      {
        g.translate(canvasWidth - LABEL_EAST, 0);
        drawEastScale(g, startRes, endx, ypos);
        g.translate(-(canvasWidth - LABEL_EAST), 0);
      }

      g.translate(LABEL_WEST, 0);

      if (av.getScaleAboveWrapped())
      {
        drawNorthScale(g, startRes, endx, ypos);
      }
      if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
      {
        g.setColor(Color.blue);
        int res;
        for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
                .size(); i++)
        {
          res = av.getColumnSelection().findHiddenRegionPosition(i)
                  - startRes;

          if (res < 0 || res > endx - startRes)
          {
            continue;
          }

          gg.fillPolygon(new int[]
          { res * avcharWidth - avcharHeight / 4,
              res * avcharWidth + avcharHeight / 4, res * avcharWidth },
                  new int[]
                  { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2),
                      ypos - (avcharHeight / 2) + 8 }, 3);

        }
      }

      if (g.getClip() == null)
      {
        g.setClip(0, 0, cWidth * avcharWidth, canvasHeight);
      }

      drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
      g.setClip(null);

      if (av.isShowAnnotation())
      {
        g.translate(0, cHeight + ypos + 4);
        if (annotations == null)
        {
          annotations = new AnnotationPanel(av);
        }

        annotations.drawComponent(g, startRes, endx + 1);
        g.translate(0, -cHeight - ypos - 4);
      }
      g.translate(-LABEL_WEST, 0);

      ypos += cHeight + getAnnotationHeight() + hgap;

      startRes += cWidth;
    }

  }

  AnnotationPanel annotations;

  int getAnnotationHeight()
  {
    if (!av.isShowAnnotation())
    {
      return 0;
    }

    if (annotations == null)
    {
      annotations = new AnnotationPanel(av);
    }

    return annotations.adjustPanelHeight();
  }

  private void drawPanel(Graphics g1, int startRes, int endRes,
          int startSeq,
          int endSeq, int offset)
  {


    if (!av.hasHiddenColumns())
    {
      draw(g1, startRes, endRes, startSeq, endSeq, offset);
    }
    else
    {

      int screenY = 0;
      int blockStart = startRes;
      int blockEnd = endRes;

      if (av.hasHiddenColumns())
      {
        for (int[] region : av.getColumnSelection().getHiddenColumns())
        {
          int hideStart = region[0];
          int hideEnd = region[1];

          if (hideStart <= blockStart)
          {
            blockStart += (hideEnd - hideStart) + 1;
            continue;
          }

          blockEnd = hideStart - 1;

          g1.translate(screenY * avcharWidth, 0);

          draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);

          if (av.getShowHiddenMarkers())
          {
            g1.setColor(Color.blue);
            g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
                    0 + offset, (blockEnd - blockStart + 1) * avcharWidth
                            - 1, (endSeq - startSeq) * avcharHeight
                            + offset);
          }

          g1.translate(-screenY * avcharWidth, 0);
          screenY += blockEnd - blockStart + 1;
          blockStart = hideEnd + 1;
        }
      }
      if (screenY <= (endRes - startRes))
      {
        blockEnd = blockStart + (endRes - startRes) - screenY;
        g1.translate(screenY * avcharWidth, 0);
        draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);

        g1.translate(-screenY * avcharWidth, 0);
      }
    }

  }

  // int startRes, int endRes, int startSeq, int endSeq, int x, int y,
  // int x1, int x2, int y1, int y2, int startx, int starty,
  void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq,
          int offset)
  {
    g.setFont(av.getFont());
    sr.prepare(g, av.isRenderGaps());
    updateViewport();
    SequenceI nextSeq;

    // / First draw the sequences
    // ///////////////////////////
    for (int i = startSeq; i < endSeq; i++)
    {
      nextSeq = av.getAlignment().getSequenceAt(i);

      if (nextSeq == null)
      {
        continue;
      }

      sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
              startRes, endRes, offset + ((i - startSeq) * avcharHeight));

      if (av.isShowSequenceFeatures())
      {
        fr.drawSequence(g, nextSeq, startRes, endRes, offset
                + ((i - startSeq) * avcharHeight));
      }

      // / Highlight search Results once all sequences have been drawn
      // ////////////////////////////////////////////////////////
      if (searchResults != null)
      {
        int[] visibleResults = searchResults.getResults(nextSeq, startRes,
                endRes);
        if (visibleResults != null)
        {
          for (int r = 0; r < visibleResults.length; r += 2)
          {
            sr.drawHighlightedText(nextSeq, visibleResults[r],
                    visibleResults[r + 1], (visibleResults[r] - startRes)
                            * avcharWidth, offset
                            + ((i - startSeq) * avcharHeight));
          }
        }
      }

      if (av.cursorMode && cursorY == i && cursorX >= startRes
              && cursorX <= endRes)
      {
        sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * avcharWidth,
                offset + ((i - startSeq) * avcharHeight));
      }
    }

    if (av.getSelectionGroup() != null
            || av.getAlignment().getGroups().size() > 0)
    {
      drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
    }

  }

  private void drawGroupsBoundaries(Graphics g, int startRes, int endRes,
          int startSeq, int endSeq, int offset)
  {
    //
    // ///////////////////////////////////
    // Now outline any areas if necessary
    // ///////////////////////////////////
    SequenceGroup group = av.getSelectionGroup();

    int sx = -1;
    int sy = -1;
    int ex = -1;
    int groupIndex = -1;

    if ((group == null) && (av.getAlignment().getGroups().size() > 0))
    {
      group = av.getAlignment().getGroups().get(0);
      groupIndex = 0;
    }

    if (group != null)
    {
      do
      {
        int oldY = -1;
        int i = 0;
        boolean inGroup = false;
        int top = -1;
        int bottom = -1;
        int alHeight = av.getAlignment().getHeight() - 1;

        for (i = startSeq; i < endSeq; i++)
        {
          sx = (group.getStartRes() - startRes) * avcharWidth;
          sy = offset + ((i - startSeq) * avcharHeight);
          ex = (((group.getEndRes() + 1) - group.getStartRes()) * avcharWidth) - 1;

          if (sx + ex < 0 || sx > imgWidth)
          {
            continue;
          }

          if ((sx <= (endRes - startRes) * avcharWidth)
                  && group.getSequences(null).contains(
                          av.getAlignment().getSequenceAt(i)))
          {
            if ((bottom == -1)
                    && (i >= alHeight || !group.getSequences(null)
                            .contains(
                                    av.getAlignment().getSequenceAt(i + 1))))
            {
              bottom = sy + avcharHeight;
            }

            if (!inGroup)
            {
              if (((top == -1) && (i == 0))
                      || !group.getSequences(null).contains(
                              av.getAlignment().getSequenceAt(i - 1)))
              {
                top = sy;
              }

              oldY = sy;
              inGroup = true;

              if (group == av.getSelectionGroup())
              {
                g.setColor(Color.red);
              }
              else
              {
                g.setColor(group.getOutlineColour());
              }
            }
          }
          else
          {
            if (inGroup)
            {
              if (sx >= 0 && sx < imgWidth)
              {
                g.drawLine(sx, oldY, sx, sy);
              }

              if (sx + ex < imgWidth)
              {
                g.drawLine(sx + ex, oldY, sx + ex, sy);
              }

              if (sx < 0)
              {
                ex += sx;
                sx = 0;
              }

              if (sx + ex > imgWidth)
              {
                ex = imgWidth;
              }

              else if (sx + ex >= (endRes - startRes + 1) * avcharWidth)
              {
                ex = (endRes - startRes + 1) * avcharWidth;
              }

              if (top != -1)
              {
                g.drawLine(sx, top, sx + ex, top);
                top = -1;
              }

              if (bottom != -1)
              {
                g.drawLine(sx, bottom, sx + ex, bottom);
                bottom = -1;
              }

              inGroup = false;
            }
          }
        }

        if (inGroup)
        {
          sy = offset + ((i - startSeq) * avcharHeight);
          if (sx >= 0 && sx < imgWidth)
          {
            g.drawLine(sx, oldY, sx, sy);
          }

          if (sx + ex < imgWidth)
          {
            g.drawLine(sx + ex, oldY, sx + ex, sy);
          }

          if (sx < 0)
          {
            ex += sx;
            sx = 0;
          }

          if (sx + ex > imgWidth)
          {
            ex = imgWidth;
          }
          else if (sx + ex >= (endRes - startRes + 1) * avcharWidth)
          {
            ex = (endRes - startRes + 1) * avcharWidth;
          }

          if (top != -1)
          {
            g.drawLine(sx, top, sx + ex, top);
            top = -1;
          }

          if (bottom != -1)
          {
            g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
            bottom = -1;
          }

          inGroup = false;
        }

        groupIndex++;

        if (groupIndex >= av.getAlignment().getGroups().size())
        {
          break;
        }

        group = av.getAlignment().getGroups()
                .get(groupIndex);
      } while (groupIndex < av.getAlignment().getGroups().size());

    }
  }

  public void highlightSearchResults(SearchResults results)
  {
    searchResults = results;

    repaint();
  }

}