/*
 * 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.gui;

import jalview.datamodel.SequenceI;
import jalview.renderer.AnnotationRenderer;
import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.viewmodel.OverviewDimensions;

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;

/**
 * Panel displaying an overview of the full alignment, with an interactive box
 * representing the viewport onto the alignment.
 * 
 * @author $author$
 * @version $Revision$
 */
public class OverviewPanel extends JPanel implements Runnable
{
  private static final Color TRANS_GREY = new Color(100, 100, 100, 25);

  private final AnnotationRenderer renderer = new AnnotationRenderer();

  private OverviewDimensions od;

  private BufferedImage miniMe;

  private BufferedImage lastMiniMe = null;

  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;

  jalview.renderer.seqfeatures.FeatureRenderer fr;

  /**
   * Creates a new OverviewPanel object.
   * 
   * @param alPanel
   *          The alignment panel which is shown in the overview panel
   */
  public OverviewPanel(AlignmentPanel alPanel)
  {
    this.av = alPanel.av;
    this.ap = alPanel;
    setLayout(null);

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

    od = new OverviewDimensions(av.getRanges(),
            (av.isShowAnnotation() && av
                    .getAlignmentConservationAnnotation() != null));

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

    addMouseMotionListener(new MouseMotionAdapter()
    {
      @Override
      public void mouseDragged(MouseEvent evt)
      {
        if (!av.getWrapAlignment())
        {
          od.updateViewportFromMouse(evt.getX(), evt.getY(), av
                  .getAlignment().getHiddenSequences(), av
                  .getColumnSelection(), av.getRanges());
          ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
        }
      }
    });

    addMouseListener(new MouseAdapter()
    {
      @Override
      public void mousePressed(MouseEvent evt)
      {
        if (!av.getWrapAlignment())
        {
          od.updateViewportFromMouse(evt.getX(), evt.getY(), av
                  .getAlignment().getHiddenSequences(), av
                  .getColumnSelection(), av.getRanges());
          ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
        }
      }
    });

    updateOverviewImage();
  }

  /**
   * Updates the overview image when the related alignment panel is updated
   */
  public void updateOverviewImage()
  {
    if (resizing)
    {
      resizeAgain = true;
      return;
    }

    resizing = true;

    if ((getWidth() > 0) && (getHeight() > 0))
    {
      od.setWidth(getWidth());
      od.setHeight(getHeight());
    }

    setPreferredSize(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.getSeqPanel().seqCanvas.getFeatureRenderer());
    }

    // why do we need to set preferred size again? was set in
    // updateOverviewImage
    setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));

    miniMe = new BufferedImage(od.getWidth(), od.getHeight(),
            BufferedImage.TYPE_INT_RGB);

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

    // calculate sampleCol and sampleRow
    // alignment width is max number of residues/bases
    // alignment height is number of sequences
    int alwidth = av.getAlignment().getWidth();
    int alheight = av.getAlignment().getAbsoluteHeight();

    // sampleCol or sampleRow is the width/height allocated to each residue
    // in particular, sometimes we may need more than one row/col of the
    // BufferedImage allocated
    // sampleCol is how much of a residue to assign to each pixel
    // sampleRow is how many sequences to assign to each pixel
    float sampleCol = alwidth / (float) od.getWidth();
    float sampleRow = alheight / (float) od.getSequencesHeight();

    buildImage(sampleRow, sampleCol);

    // check for conservation annotation to make sure overview works for DNA too
    if (av.isShowAnnotation()
            && (av.getAlignmentConservationAnnotation() != null))
    {
      renderer.updateFromAlignViewport(av);
      for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
      {
        mg.translate(col, od.getSequencesHeight());
        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;

    if (resizeAgain)
    {
      resizeAgain = false;
      updateOverviewImage();
    }
    else
    {
      lastMiniMe = miniMe;
    }

    setBoxPosition();
  }

  /*
   * Build the overview panel image
   */
  private void buildImage(float sampleRow, float sampleCol)
  {
    int lastcol = -1;
    int lastrow = -1;
    int rgbColour = Color.white.getRGB();

    SequenceI seq = null;
    FeatureColourFinder finder = new FeatureColourFinder(fr);

    final boolean hasHiddenCols = av.hasHiddenColumns();
    boolean hiddenRow = false;
    // get hidden row and hidden column map once at beginning.
    // clone featureRenderer settings to avoid race conditions... if state is
    // updated just need to refresh again
    for (int row = 0; row < od.getSequencesHeight() && !resizeAgain; row++)
    {
      boolean doCopy = true;
      int currentrow = (int) (row * sampleRow);
      if (currentrow != lastrow)
      {
        doCopy = false;

        lastrow = currentrow;

        // get the sequence which would be at alignment index 'lastrow' if no
        // rows were hidden, and determine whether it is hidden or not
        hiddenRow = av.getAlignment().isHidden(lastrow);
        seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow);
      }

      for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
      {
        if (doCopy)
        {
          rgbColour = miniMe.getRGB(col, row - 1);
        }
        else if ((int) (col * sampleCol) != lastcol
                || (int) (row * sampleRow) != lastrow)
        {
          lastcol = (int) (col * sampleCol);
          rgbColour = getColumnColourFromSequence(seq, hiddenRow,
                  hasHiddenCols, lastcol, finder);
        }
        // else we just use the color we already have , so don't need to set it

        miniMe.setRGB(col, row, rgbColour);
      }
    }
  }

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

    if ((seq != null) && (seq.getLength() > lastcol))
    {
    	color = sr.getResidueColour(seq, lastcol, finder);
    }

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

    return color.getRGB();
  }

  /**
   * Update the overview panel box when the associated alignment panel is
   * changed
   * 
   */
  public void setBoxPosition()
  {
    od.setBoxPosition(av.getAlignment()
            .getHiddenSequences(), av.getColumnSelection(), av.getRanges());
    repaint();
  }


  @Override
  public void paintComponent(Graphics g)
  {
    if (resizing || resizeAgain)
    {
      if (lastMiniMe == null)
      {
        g.setColor(Color.white);
        g.fillRect(0, 0, getWidth(), getHeight());
      }
      else
      {
        g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
      }
      g.setColor(TRANS_GREY);
      g.fillRect(0, 0, getWidth(), getHeight());
    }
    else if (lastMiniMe != null)
    {
      g.drawImage(lastMiniMe, 0, 0, this);
      if (lastMiniMe != miniMe)
      {
        g.setColor(TRANS_GREY);
        g.fillRect(0, 0, getWidth(), getHeight());
      }
    }

    g.setColor(Color.red);
    od.drawBox(g);
  }
}