/*
 * 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.api.RotatableCanvasI;
import jalview.datamodel.Point;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequencePoint;
import jalview.math.RotatableMatrix;
import jalview.math.RotatableMatrix.Axis;
import jalview.util.ColorUtils;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;

import java.awt.Color;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.Image;
import java.awt.RenderingHints;
import java.awt.event.InputEvent;
import java.awt.event.KeyEvent;
import java.awt.event.KeyListener;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
import java.awt.event.MouseWheelEvent;
import java.awt.event.MouseWheelListener;
import java.util.Vector;

import javax.swing.JPanel;
import javax.swing.ToolTipManager;

/**
 * Models a Panel on which a set of points, and optionally x/y/z axes, can be
 * drawn, and rotated or zoomed with the mouse
 */
public class RotatableCanvas extends JPanel implements MouseListener,
        MouseMotionListener, KeyListener, RotatableCanvasI
{
  private static final int DIMS = 3;

  // RubberbandRectangle rubberband;
  boolean drawAxes = true;

  int mouseX = 0;

  int mouseY = 0;

  Image img;

  Graphics ig;

  Dimension prefsize;

  Point centre;

  float[] width = new float[DIMS];

  float[] max = new float[DIMS];

  float[] min = new float[DIMS];

  float maxwidth;

  float scale;

  int npoint;

  Vector<SequencePoint> points;

  Point[] orig;

  Point[] axisEndPoints;

  int startx;

  int starty;

  int lastx;

  int lasty;

  int rectx1;

  int recty1;

  int rectx2;

  int recty2;

  float scalefactor = 1;

  AlignmentViewport av;

  AlignmentPanel ap;

  boolean showLabels = false;

  Color bgColour = Color.black;

  boolean applyToAllViews = false;

  boolean first = true;

  /**
   * Constructor
   * 
   * @param panel
   */
  public RotatableCanvas(AlignmentPanel panel)
  {
    this.av = panel.av;
    this.ap = panel;
    axisEndPoints = new Point[DIMS];

    addMouseWheelListener(new MouseWheelListener()
    {
      @Override
      public void mouseWheelMoved(MouseWheelEvent e)
      {
        double wheelRotation = e.getPreciseWheelRotation();
        if (wheelRotation > 0)
        {
          /*
           * zoom in
           */
          scale = (float) (scale * 1.1);
          repaint();
        }
        else if (wheelRotation < 0)
        {
          /*
           * zoom out
           */
          scale = (float) (scale * 0.9);
          repaint();
        }
      }
    });

  }

  /**
   * Refreshes the display with labels shown (or not)
   * 
   * @param show
   */
  public void showLabels(boolean show)
  {
    showLabels = show;
    repaint();
  }

  @Override
  public void setPoints(Vector<SequencePoint> points, int npoint)
  {
    this.points = points;
    this.npoint = npoint;
    if (first)
    {
      ToolTipManager.sharedInstance().registerComponent(this);
      ToolTipManager.sharedInstance().setInitialDelay(0);
      ToolTipManager.sharedInstance().setDismissDelay(10000);
    }
    prefsize = getPreferredSize();
    orig = new Point[npoint];

    for (int i = 0; i < npoint; i++)
    {
      SequencePoint sp = points.elementAt(i);
      orig[i] = sp.coord;
    }

    resetAxes();

    findCentre();
    findWidth();

    scale = findScale();
    if (first)
    {
      addMouseListener(this);
      addMouseMotionListener(this);
    }
    first = false;
  }

  /**
   * Resets axes to the initial state: x-axis to the right, y-axis up, z-axis to
   * back (so obscured in a 2-D display)
   */
  protected void resetAxes()
  {
    axisEndPoints[0] = new Point(1f, 0f, 0f);
    axisEndPoints[1] = new Point(0f, 1f, 0f);
    axisEndPoints[2] = new Point(0f, 0f, 1f);
  }

  /**
   * Computes and saves the maximum and minimum (x, y, z) positions of any
   * sequence point, and also the min-max range (width) for each dimension, and
   * the maximum width for all dimensions
   */
  protected void findWidth()
  {
    max = new float[DIMS];
    min = new float[DIMS];

    max[0] = Float.MIN_VALUE;
    max[1] = Float.MIN_VALUE;
    max[2] = Float.MIN_VALUE;

    min[0] = Float.MAX_VALUE;
    min[1] = Float.MAX_VALUE;
    min[2] = Float.MAX_VALUE;

    for (SequencePoint sp : points)
    {
      max[0] = Math.max(max[0], sp.coord.x);
      max[1] = Math.max(max[1], sp.coord.y);
      max[2] = Math.max(max[2], sp.coord.z);
      min[0] = Math.min(min[0], sp.coord.x);
      min[1] = Math.min(min[1], sp.coord.y);
      min[2] = Math.min(min[2], sp.coord.z);
    }

    width[0] = Math.abs(max[0] - min[0]);
    width[1] = Math.abs(max[1] - min[1]);
    width[2] = Math.abs(max[2] - min[2]);

    maxwidth = Math.max(width[0], Math.max(width[1], width[2]));
  }

  /**
   * DOCUMENT ME!
   * 
   * @return DOCUMENT ME!
   */
  protected float findScale()
  {
    int dim;
    int w;
    int height;

    if (getWidth() != 0)
    {
      w = getWidth();
      height = getHeight();
    }
    else
    {
      w = prefsize.width;
      height = prefsize.height;
    }

    if (w < height)
    {
      dim = w;
    }
    else
    {
      dim = height;
    }

    return (dim * scalefactor) / (2 * maxwidth);
  }

  /**
   * Computes and saves the position of the centre of the view
   */
  protected void findCentre()
  {
    findWidth();

    float x = (max[0] + min[0]) / 2;
    float y = (max[1] + min[1]) / 2;
    float z = (max[2] + min[2]) / 2;

    centre = new Point(x, y, z);
  }

  /**
   * DOCUMENT ME!
   * 
   * @return DOCUMENT ME!
   */
  @Override
  public Dimension getPreferredSize()
  {
    if (prefsize != null)
    {
      return prefsize;
    }
    else
    {
      return new Dimension(400, 400);
    }
  }

  /**
   * DOCUMENT ME!
   * 
   * @return DOCUMENT ME!
   */
  @Override
  public Dimension getMinimumSize()
  {
    return getPreferredSize();
  }

  /**
   * DOCUMENT ME!
   * 
   * @param g
   *          DOCUMENT ME!
   */
  @Override
  public void paintComponent(Graphics g1)
  {

    Graphics2D g = (Graphics2D) g1;

    g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
            RenderingHints.VALUE_ANTIALIAS_ON);
    if (points == null)
    {
      g.setFont(new Font("Verdana", Font.PLAIN, 18));
      g.drawString(
              MessageManager.getString("label.calculating_pca") + "....",
              20, getHeight() / 2);
    }
    else
    {
      // Only create the image at the beginning -
      if ((img == null) || (prefsize.width != getWidth())
              || (prefsize.height != getHeight()))
      {
        prefsize.width = getWidth();
        prefsize.height = getHeight();

        scale = findScale();

        // System.out.println("New scale = " + scale);
        img = createImage(getWidth(), getHeight());
        ig = img.getGraphics();
      }

      drawBackground(ig, bgColour);
      drawScene(ig);

      if (drawAxes)
      {
        drawAxes(ig);
      }

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

  /**
   * Resets the view to initial state (no rotation)
   */
  public void resetView()
  {
    img = null;
    resetAxes();
  }

  /**
   * Draws lines for the x, y, z axes
   * 
   * @param g
   */
  public void drawAxes(Graphics g)
  {

    g.setColor(Color.yellow);

    for (int i = 0; i < DIMS; i++)
    {
      g.drawLine(getWidth() / 2, getHeight() / 2,
              (int) ((axisEndPoints[i].x * scale * max[0]) + (getWidth() / 2)),
              (int) ((axisEndPoints[i].y * scale * max[1]) + (getHeight() / 2)));
    }
  }

  /**
   * Fills the background with the specified colour
   * 
   * @param g
   * @param col
   */
  public void drawBackground(Graphics g, Color col)
  {
    g.setColor(col);
    g.fillRect(0, 0, prefsize.width, prefsize.height);
  }

  /**
   * Draws points (6x6 squares) for the sequences of the PCA, and labels
   * (sequence names) if configured to do so. The sequence points colours are
   * taken from the sequence ids in the alignment (converting black to white).
   * Sequences 'at the back' (z-coordinate is negative) are shaded slightly
   * darker to help give a 3-D sensation.
   * 
   * @param g
   */
  public void drawScene(Graphics g1)
  {
    Graphics2D g = (Graphics2D) g1;

    g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
            RenderingHints.VALUE_ANTIALIAS_ON);

    for (int i = 0; i < npoint; i++)
    {
      /*
       * sequence point colour as sequence id, but
       * gray if sequence is currently selected
       */
      SequencePoint sp = points.elementAt(i);
      Color sequenceColour = getSequencePointColour(sp);
      g.setColor(sequenceColour);

      int halfwidth = getWidth() / 2;
      int halfheight = getHeight() / 2;
      int x = (int) ((sp.coord.x - centre.x) * scale) + halfwidth;
      int y = (int) ((sp.coord.y - centre.y) * scale) + halfheight;
      g.fillRect(x - 3, y - 3, 6, 6);

      if (showLabels)
      {
        g.setColor(Color.red);
        g.drawString(sp.getSequence().getName(), x - 3, y - 4);
      }
    }

    // //Now the rectangle
    // if (rectx2 != -1 && recty2 != -1) {
    // g.setColor(Color.white);
    //
    // g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);
    // }
  }

  /**
   * Determines the colour to use when drawing a sequence point. The colour is
   * taken from the sequence id, with black converted to white, and then
   * graduated from darker (at the back) to brighter (at the front) based on the
   * z-axis coordinate of the point.
   * 
   * @param sp
   * @return
   */
  protected Color getSequencePointColour(SequencePoint sp)
  {
    SequenceI sequence = sp.getSequence();
    Color sequenceColour = av.getSequenceColour(sequence);
    if (sequenceColour == Color.black)
    {
      sequenceColour = Color.white;
    }
    if (av.getSelectionGroup() != null)
    {
      if (av.getSelectionGroup().getSequences(null).contains(sequence))
      {
        sequenceColour = Color.gray;
      }
    }

    /*
     * graduate from front (brighter) to back (darker)
     */
    sequenceColour = ColorUtils.getGraduatedColour(sp.coord.z, min[2],
            max[2], sequenceColour);

    return sequenceColour;
  }

  @Override
  public void keyTyped(KeyEvent evt)
  {
  }

  @Override
  public void keyReleased(KeyEvent evt)
  {
  }

  /**
   * Responds to up or down arrow key by zooming in or out, respectively
   * 
   * @param evt
   */
  @Override
  public void keyPressed(KeyEvent evt)
  {
    if (evt.getKeyCode() == KeyEvent.VK_UP)
    {
      scalefactor = (float) (scalefactor * 1.1);
      scale = findScale();
    }
    else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
    {
      scalefactor = (float) (scalefactor * 0.9);
      scale = findScale();
    }
    else if (evt.getKeyChar() == 's')
    {
      // Cache.log.warn("DEBUG: Rectangle selection");
      // todo not yet enabled as rectx2, recty2 are always -1
      // need to set them in mouseDragged
      if ((rectx2 != -1) && (recty2 != -1))
      {
        rectSelect(rectx1, recty1, rectx2, recty2);
      }
    }

    repaint();
  }

  @Override
  public void mouseClicked(MouseEvent evt)
  {
  }

  @Override
  public void mouseEntered(MouseEvent evt)
  {
  }

  @Override
  public void mouseExited(MouseEvent evt)
  {
  }

  @Override
  public void mouseReleased(MouseEvent evt)
  {
  }

  /**
   * If the mouse press is at (within 2 pixels of) a sequence point, toggles
   * (adds or removes) the corresponding sequence as a member of the viewport
   * selection group. This supports configuring a group in the alignment by
   * clicking on points in the PCA display.
   */
  @Override
  public void mousePressed(MouseEvent evt)
  {
    int x = evt.getX();
    int y = evt.getY();

    mouseX = x;
    mouseY = y;

    startx = x;
    starty = y;

    rectx1 = x;
    recty1 = y;

    rectx2 = -1;
    recty2 = -1;

    SequenceI found = findSequenceAtPoint(x, y);

    if (found != null)
    {
      AlignmentPanel[] aps = getAssociatedPanels();

      for (int a = 0; a < aps.length; a++)
      {
        if (aps[a].av.getSelectionGroup() != null)
        {
          aps[a].av.getSelectionGroup().addOrRemove(found, true);
        }
        else
        {
          aps[a].av.setSelectionGroup(new SequenceGroup());
          aps[a].av.getSelectionGroup().addOrRemove(found, true);
          aps[a].av.getSelectionGroup()
                  .setEndRes(aps[a].av.getAlignment().getWidth() - 1);
        }
      }
      PaintRefresher.Refresh(this, av.getSequenceSetId());
      // canonical selection is sent to other listeners
      av.sendSelection();
    }

    repaint();
  }

  /**
   * Sets the tooltip to the name of the sequence within 2 pixels of the mouse
   * position, or clears the tooltip if none found
   */
  @Override
  public void mouseMoved(MouseEvent evt)
  {
    SequenceI found = findSequenceAtPoint(evt.getX(), evt.getY());

    this.setToolTipText(found == null ? null : found.getName());
  }

  /**
   * Action handler for a mouse drag. Rotates the display around the X axis (for
   * up/down mouse movement) and/or the Y axis (for left/right mouse movement).
   * 
   * @param evt
   */
  @Override
  public void mouseDragged(MouseEvent evt)
  {
    int xPos = evt.getX();
    int yPos = evt.getY();

    if (xPos == mouseX && yPos == mouseY)
    {
      return;
    }

    // Check if this is a rectangle drawing drag
    if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) != 0)
    {
      // rectx2 = evt.getX();
      // recty2 = evt.getY();
    }
    else
    {
      /*
       * get the identity transformation...
       */
      RotatableMatrix rotmat = new RotatableMatrix();

      /*
       * rotate around the X axis for change in Y
       * (mouse movement up/down); note we are equating a
       * number of pixels with degrees of rotation here!
       */
      if (yPos != mouseY)
      {
        rotmat.rotate(yPos - mouseY, Axis.X);
      }

      /*
       * rotate around the Y axis for change in X
       * (mouse movement left/right)
       */
      if (xPos != mouseX)
      {
        rotmat.rotate(xPos - mouseX, Axis.Y);
      }

      /*
       * apply the composite transformation to sequence points
       */
      for (int i = 0; i < npoint; i++)
      {
        SequencePoint sp = points.elementAt(i);
        sp.translateBack(centre);

        // Now apply the rotation matrix
        sp.coord = rotmat.vectorMultiply(sp.coord);

        // Now translate back again
        sp.translate(centre);
      }

      /*
       * rotate the x/y/z axis positions
       */
      for (int i = 0; i < DIMS; i++)
      {
        axisEndPoints[i] = rotmat.vectorMultiply(axisEndPoints[i]);
      }

      mouseX = xPos;
      mouseY = yPos;

      paint(this.getGraphics());
    }
  }

  /**
   * Adds any sequences whose displayed points are within the given rectangle to
   * the viewport's current selection. Intended for key 's' after dragging to
   * select a region of the PCA.
   * 
   * @param x1
   * @param y1
   * @param x2
   * @param y2
   */
  protected void rectSelect(int x1, int y1, int x2, int y2)
  {
    for (int i = 0; i < npoint; i++)
    {
      SequencePoint sp = points.elementAt(i);
      int tmp1 = (int) (((sp.coord.x - centre.x) * scale)
              + (getWidth() / 2.0));
      int tmp2 = (int) (((sp.coord.y - centre.y) * scale)
              + (getHeight() / 2.0));

      if ((tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2))
      {
        if (av != null)
        {
          SequenceI sequence = sp.getSequence();
          if (!av.getSelectionGroup().getSequences(null)
                  .contains(sequence))
          {
            av.getSelectionGroup().addSequence(sequence, true);
          }
        }
      }
    }
  }

  /**
   * Answers the first sequence found whose point on the display is within 2
   * pixels of the given coordinates, or null if none is found
   * 
   * @param x
   * @param y
   * 
   * @return
   */
  protected SequenceI findSequenceAtPoint(int x, int y)
  {
    int halfwidth = getWidth() / 2;
    int halfheight = getHeight() / 2;

    int found = -1;

    for (int i = 0; i < npoint; i++)
    {
      SequencePoint sp = points.elementAt(i);
      int px = (int) ((sp.coord.x - centre.x) * scale)
              + halfwidth;
      int py = (int) ((sp.coord.y - centre.y) * scale)
              + halfheight;

      if ((Math.abs(px - x) < 3) && (Math.abs(py - y) < 3))
      {
        found = i;
        break;
      }
    }

    if (found != -1)
    {
      return points.elementAt(found).getSequence();
    }
    else
    {
      return null;
    }
  }

  /**
   * Answers the panel the PCA is associated with (all panels for this alignment
   * if 'associate with all panels' is selected).
   * 
   * @return
   */
  AlignmentPanel[] getAssociatedPanels()
  {
    if (applyToAllViews)
    {
      return PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
    }
    else
    {
      return new AlignmentPanel[] { ap };
    }
  }
}