/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
 * Copyright (C) 2015 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.gui;

import jalview.renderer.AnnotationRenderer;

import java.awt.Color;
import java.awt.Dimension;
import java.awt.Graphics;
import java.awt.event.ComponentAdapter;
import java.awt.event.ComponentEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.awt.event.MouseMotionAdapter;
import java.awt.image.BufferedImage;

import javax.swing.JPanel;

/**
 * DOCUMENT ME!
 * 
 * @author $author$
 * @version $Revision$
 */
public class OverviewPanel extends JPanel implements Runnable
{
  BufferedImage miniMe;

  AlignViewport av;

  AlignmentPanel ap;

  final AnnotationRenderer renderer = new AnnotationRenderer();

  float scalew = 1f;

  float scaleh = 1f;

  int width;

  int sequencesHeight;

  int graphHeight = 20;

  int boxX = -1;

  int boxY = -1;

  int boxWidth = -1;

  int boxHeight = -1;

  boolean resizing = false;

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

  jalview.renderer.seqfeatures.FeatureRenderer fr;

  /**
   * Creates a new OverviewPanel object.
   * 
   * @param ap
   *          DOCUMENT ME!
   */
  public OverviewPanel(AlignmentPanel ap)
  {
    this.av = ap.av;
    this.ap = ap;
    setLayout(null);

    sr = new SequenceRenderer(av);
    sr.renderGaps = false;
    sr.forOverview = true;
    fr = new FeatureRenderer(ap);

    // scale the initial size of overviewpanel to shape of alignment
    float initialScale = (float) av.getAlignment().getWidth()
            / (float) av.getAlignment().getHeight();

    if (av.getAlignmentConservationAnnotation() == null)
    {
      graphHeight = 0;
    }

    if (av.getAlignment().getWidth() > av.getAlignment().getHeight())
    {
      // wider
      width = 400;
      sequencesHeight = (int) (400f / initialScale);
      if (sequencesHeight < 40)
      {
        sequencesHeight = 40;
      }
    }
    else
    {
      // taller
      width = (int) (400f * initialScale);
      sequencesHeight = 300;

      if (width < 120)
      {
        width = 120;
      }
    }

    addComponentListener(new ComponentAdapter()
    {
      @Override
      public void componentResized(ComponentEvent evt)
      {
        if ((getWidth() != width)
                || (getHeight() != (sequencesHeight + graphHeight)))
        {
          updateOverviewImage();
        }
      }
    });

    addMouseMotionListener(new MouseMotionAdapter()
    {
      @Override
      public void mouseDragged(MouseEvent evt)
      {
        if (!av.getWrapAlignment())
        {
          // TODO: feature: jv2.5 detect shift drag and update selection from
          // it.
          boxX = evt.getX();
          boxY = evt.getY();
          checkValid();
        }
      }
    });

    addMouseListener(new MouseAdapter()
    {
      @Override
      public void mousePressed(MouseEvent evt)
      {
        if (!av.getWrapAlignment())
        {
          boxX = evt.getX();
          boxY = evt.getY();
          checkValid();
        }
      }
    });

    updateOverviewImage();
  }

  /**
   * DOCUMENT ME!
   */
  void checkValid()
  {
    if (boxY < 0)
    {
      boxY = 0;
    }

    if (boxY > (sequencesHeight - boxHeight))
    {
      boxY = sequencesHeight - boxHeight + 1;
    }

    if (boxX < 0)
    {
      boxX = 0;
    }

    if (boxX > (width - boxWidth))
    {
      if (av.hasHiddenColumns())
      {
        // Try smallest possible box
        boxWidth = (int) ((av.endRes - av.startRes + 1) * av.getCharWidth() * scalew);
      }
      boxX = width - boxWidth;
    }

    int col = (int) (boxX / scalew / av.getCharWidth());
    int row = (int) (boxY / scaleh / av.getCharHeight());

    if (av.hasHiddenColumns())
    {
      if (!av.getColumnSelection().isVisible(col))
      {
        return;
      }

      col = av.getColumnSelection().findColumnPosition(col);
    }

    if (av.hasHiddenRows())
    {
      row = av.getAlignment().getHiddenSequences()
              .findIndexWithoutHiddenSeqs(row);
    }

    ap.setScrollValues(col, row);

  }

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

    resizing = true;

    if ((getWidth() > 0) && (getHeight() > 0))
    {
      width = getWidth();
      sequencesHeight = getHeight() - graphHeight;
    }

    setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));

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

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

  /**
   * DOCUMENT ME!
   */
  @Override
  public void run()
  {
    miniMe = null;

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

    int alwidth = av.getAlignment().getWidth();
    int alheight = av.getAlignment().getHeight()
            + av.getAlignment().getHiddenSequences().getSize();

    setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));

    int fullsizeWidth = alwidth * av.getCharWidth();
    int fullsizeHeight = alheight * av.getCharHeight();

    scalew = (float) width / (float) fullsizeWidth;
    scaleh = (float) sequencesHeight / (float) fullsizeHeight;

    miniMe = new BufferedImage(width, sequencesHeight + graphHeight,
            BufferedImage.TYPE_INT_RGB);

    Graphics mg = miniMe.getGraphics();
    mg.setColor(Color.orange);
    mg.fillRect(0, 0, width, miniMe.getHeight());

    float sampleCol = (float) alwidth / (float) width;
    float sampleRow = (float) alheight / (float) sequencesHeight;

    int lastcol = -1, lastrow = -1;
    int color = Color.white.getRGB();
    int row, col;
    jalview.datamodel.SequenceI seq;
    final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
            .hasHiddenColumns();
    boolean hiddenRow = false;
    for (row = 0; row < sequencesHeight; row++)
    {
      if ((int) (row * sampleRow) == lastrow)
      {
        // No need to recalculate the colours,
        // Just copy from the row above
        for (col = 0; col < width; col++)
        {
          miniMe.setRGB(col, row, miniMe.getRGB(col, row - 1));
        }
        continue;
      }

      lastrow = (int) (row * sampleRow);

      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);
      }

      if (seq == null)
      {
        System.out.println(lastrow + " null");
        continue;
      }

      for (col = 0; col < width; col++)
      {
        if ((int) (col * sampleCol) == lastcol
                && (int) (row * sampleRow) == lastrow)
        {
          miniMe.setRGB(col, row, color);
          continue;
        }

        lastcol = (int) (col * sampleCol);

        if (seq.getLength() > lastcol)
        {
          color = sr.getResidueBoxColour(seq, lastcol).getRGB();

          if (av.isShowSequenceFeatures())
          {
            color = fr.findFeatureColour(color, seq, lastcol);
          }
        }
        else
        {
          color = -1; // White
        }

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

        miniMe.setRGB(col, row, color);

      }
    }

    if (av.getAlignmentConservationAnnotation() != null)
    {
      renderer.updateFromAlignViewport(av);
      for (col = 0; col < width; col++)
      {
        lastcol = (int) (col * sampleCol);
        {
          mg.translate(col, sequencesHeight);
          renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
                  av.getAlignmentConservationAnnotation().annotations,
                  (int) (sampleCol) + 1, graphHeight,
                  (int) (col * sampleCol), (int) (col * sampleCol) + 1);
          mg.translate(-col, -sequencesHeight);
        }
      }
    }
    System.gc();

    resizing = false;

    setBoxPosition();

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

  /**
   * DOCUMENT ME!
   */
  public void setBoxPosition()
  {
    int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth();
    int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment()
            .getHiddenSequences().getSize())
            * av.getCharHeight();

    int startRes = av.getStartRes();
    int endRes = av.getEndRes();

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

    int startSeq = av.startSeq;
    int endSeq = av.endSeq;

    if (av.hasHiddenRows())
    {
      startSeq = av.getAlignment().getHiddenSequences()
              .adjustForHiddenSeqs(startSeq);

      endSeq = av.getAlignment().getHiddenSequences()
              .adjustForHiddenSeqs(endSeq);

    }

    scalew = (float) width / (float) fullsizeWidth;
    scaleh = (float) sequencesHeight / (float) fullsizeHeight;

    boxX = (int) (startRes * av.getCharWidth() * scalew);
    boxY = (int) (startSeq * av.getCharHeight() * scaleh);

    if (av.hasHiddenColumns())
    {
      boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
    }
    else
    {
      boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
    }

    boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);

    repaint();
  }

  /**
   * DOCUMENT ME!
   * 
   * @param g
   *          DOCUMENT ME!
   */
  @Override
  public void paintComponent(Graphics g)
  {
    if (resizing)
    {
      g.setColor(Color.white);
      g.fillRect(0, 0, getWidth(), getHeight());
    }
    else if (miniMe != null)
    {
      g.drawImage(miniMe, 0, 0, this);
    }

    g.setColor(Color.red);
    g.drawRect(boxX, boxY, boxWidth, boxHeight);
    g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);

  }
}