/*
 * 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.viewmodel.OverviewDimensions;

import java.awt.Color;
import java.awt.Dimension;
import java.awt.Frame;
import java.awt.Graphics;
import java.awt.Image;
import java.awt.Panel;
import java.awt.event.ComponentAdapter;
import java.awt.event.ComponentEvent;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;

public class OverviewPanel extends Panel implements Runnable,
        MouseMotionListener, MouseListener
{
  private OverviewDimensions od;

  private Image miniMe;

  private Image offscreen;

  private AlignViewport av;

  private AlignmentPanel ap;

  private boolean resizing = false;

  // This is set true if the user resizes whilst
  // the overview is being calculated
  private boolean resizeAgain = false;

  // Can set different properties in this seqCanvas than
  // main visible SeqCanvas
  private SequenceRenderer sr;

  private FeatureRenderer fr;

  private Frame nullFrame;

  public OverviewPanel(AlignmentPanel ap)
  {
    this.av = ap.av;
    this.ap = ap;
    setLayout(null);
    nullFrame = new Frame();
    nullFrame.addNotify();

    sr = new SequenceRenderer(av);
    sr.graphics = nullFrame.getGraphics();
    sr.renderGaps = false;
    sr.forOverview = true;
    fr = new FeatureRenderer(av);

    od = new OverviewDimensions(av);

    setSize(new Dimension(od.getWidth(), od.getHeight()));
    addComponentListener(new ComponentAdapter()
    {

      @Override
      public void componentResized(ComponentEvent evt)
      {
        if ((getWidth() != od.getWidth())
                || (getHeight() != (od.getHeight())))
        {
          updateOverviewImage();
        }
      }
    });

    addMouseMotionListener(this);

    addMouseListener(this);

    updateOverviewImage();

  }

  @Override
  public void mouseEntered(MouseEvent evt)
  {
  }

  @Override
  public void mouseExited(MouseEvent evt)
  {
  }

  @Override
  public void mouseClicked(MouseEvent evt)
  {
  }

  @Override
  public void mouseMoved(MouseEvent evt)
  {
  }

  @Override
  public void mousePressed(MouseEvent evt)
  {
    od.setBoxX(evt.getX());
    od.setBoxY(evt.getY());
    checkValid();
  }

  @Override
  public void mouseReleased(MouseEvent evt)
  {
    od.setBoxX(evt.getX());
    od.setBoxY(evt.getY());
    checkValid();
  }

  @Override
  public void mouseDragged(MouseEvent evt)
  {
    od.setBoxX(evt.getX());
    od.setBoxY(evt.getY());
    checkValid();
  }

  /**
   * Check box dimensions and scroll positions and correct if necessary
   */
  private void checkValid()
  {
    od.checkValid();
    ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
    ap.paintAlignment(false);
  }

  /**
   * DOCUMENT ME!
   */
  public void updateOverviewImage()
  {
    if (resizing)
    {
      resizeAgain = true;
      return;
    }

    if (av.isShowSequenceFeatures())
    {
      fr.transferSettings(ap.seqPanel.seqCanvas.fr);
    }

    resizing = true;

    if ((getWidth() > 0) && (getHeight() > 0))
    {
      od.setWidth(getWidth()); // width = getWidth();
      od.setHeight(getHeight()); // sequencesHeight = getHeight() - graphHeight;
    }
    setSize(new Dimension(od.getWidth(), od.getHeight()));

    Thread thread = new Thread(this);
    thread.start();
    repaint();
  }

  @Override
  public void run()
  {
    miniMe = null;

    if (av.isShowSequenceFeatures())
    {
      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
    }

    if (getSize().width > 0 && getSize().height > 0)
    {
      od.setWidth(getSize().width);
      od.setHeight(getSize().height - od.getGraphHeight());
    }

    setSize(new Dimension(od.getWidth(), od.getHeight()));

    miniMe = nullFrame.createImage(od.getWidth(), od.getHeight());
    offscreen = nullFrame.createImage(od.getWidth(), od.getHeight());

    Graphics mg = miniMe.getGraphics();

    od.updateScales();

    int alwidth = av.getAlignment().getWidth();
    int alheight = av.getAlignment().getHeight()
            + av.getAlignment().getHiddenSequences().getSize();
    float sampleCol = alwidth / (float) od.getWidth();
    float sampleRow = alheight / (float) od.getSequencesHeight();

    buildImage(sampleRow, sampleCol, mg);

    if (av.getAlignmentConservationAnnotation() != null)
    {
      for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
      {
        mg.translate(col, od.getSequencesHeight());
        ap.annotationPanel.renderer.drawGraph(mg,
                av.getAlignmentConservationAnnotation(),
                av.getAlignmentConservationAnnotation().annotations,
                (int) (sampleCol) + 1, od.getGraphHeight(),
                (int) (col * sampleCol), (int) (col * sampleCol) + 1);
        mg.translate(-col, -od.getSequencesHeight());
      }
    }
    System.gc();

    resizing = false;

    setBoxPosition();

    if (resizeAgain)
    {
      resizeAgain = false;
      updateOverviewImage();
    }
  }

  private void buildImage(float sampleRow, float sampleCol, Graphics mg)
  {
    int lastcol = 0;
    int lastrow = 0;
    int xstart = 0;
    int ystart = 0;
    Color color = Color.yellow;
    int sameRow = 0;
    int sameCol = 0;

    jalview.datamodel.SequenceI seq = null;
    final boolean hasHiddenRows = av.hasHiddenRows();
    final boolean hasHiddenCols = av.hasHiddenColumns();
    boolean hiddenRow = false;

    for (int row = 0; row <= od.getSequencesHeight() && !resizeAgain; row++)
    {
      if ((int) (row * sampleRow) == lastrow)
      {
        sameRow++;
        continue;
      }
      else
      {
        // this should largely be a method in Alignment
        hiddenRow = false;
        if (hasHiddenRows)
        {
          seq = av.getAlignment().getHiddenSequences()
                  .getHiddenSequence(lastrow);
          if (seq == null)
          {
            int index = av.getAlignment().getHiddenSequences()
                    .findIndexWithoutHiddenSeqs(lastrow);

            seq = av.getAlignment().getSequenceAt(index);
          }
          else
          {
            hiddenRow = true;
          }
        }
        else
        {
          seq = av.getAlignment().getSequenceAt(lastrow);
        }
        // end of Alignment method

        for (int col = 0; col < od.getWidth(); col++)
        {
          if ((int) (col * sampleCol) == lastcol
                  && (int) (row * sampleRow) == lastrow)
          {
            sameCol++;
          }
          else
          {
            lastcol = (int) (col * sampleCol);

            color = getColumnColourFromSequence(seq, hiddenRow,
                    hasHiddenCols, lastcol);

            mg.setColor(color);
            if (sameCol == 1 && sameRow == 1)
            {
              mg.drawLine(xstart, ystart, xstart, ystart);
            }
            else
            {
              mg.fillRect(xstart, ystart, sameCol, sameRow);
            }

            xstart = col;
            sameCol = 1;
          }
        }
        lastrow = (int) (row * sampleRow);
        ystart = row;
        sameRow = 1;
      }
    }

  }

  /*
   * Find the colour of a sequence at a specified column position
   */
  private Color getColumnColourFromSequence(
          jalview.datamodel.SequenceI seq, boolean hiddenRow,
          boolean hasHiddenCols, int lastcol)
  {
    Color color;
    if (seq.getLength() > lastcol)
    {
      color = sr.getResidueBoxColour(seq, lastcol);

      if (av.isShowSequenceFeatures())
      {
        color = fr.findFeatureColour(color, seq, lastcol);
      }
    }
    else
    {
      color = Color.white; // White
    }

    if (hiddenRow
            || (hasHiddenCols && !av.getColumnSelection()
                    .isVisible(lastcol)))
    {
      color = color.darker().darker();
    }
    return color;
  }

  /**
   * Update the overview panel box when the associated alignment panel is
   * changed
   * 
   */
  public void setBoxPosition()
  {
    od.setBoxPosition();
    repaint();
  }

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

  @Override
  public void paint(Graphics g)
  {
    Graphics og = offscreen.getGraphics();
    if (miniMe != null)
    {
      og.drawImage(miniMe, 0, 0, this);
      og.setColor(Color.red);
      og.drawRect(od.getBoxX(), od.getBoxY(), od.getBoxWidth(),
              od.getBoxHeight());
      og.drawRect(od.getBoxX() + 1, od.getBoxY() + 1, od.getBoxWidth() - 2,
              od.getBoxHeight() - 2);
      g.drawImage(offscreen, 0, 0, this);
    }
  }

}