/**
 * 
 */
package jalview.renderer;

import java.awt.Color;
import java.awt.Graphics;

import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.ContactListI;
import jalview.datamodel.ContactRange;
import jalview.datamodel.HiddenColumns;
import jalview.renderer.api.AnnotationRowRendererI;

/**
 * @author jprocter
 *
 */
public class ContactMapRenderer implements AnnotationRowRendererI
{

  @Override
  public void renderRow(Graphics g, int charWidth, int charHeight,
          boolean hasHiddenColumns, AlignViewportI viewport,
          HiddenColumns hiddenColumns, ColumnSelection columnSelection,
          AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes,
          int eRes, float min, float max, int y)
  {
    if (sRes > aa_annotations.length)
    {
      return;
    }
    eRes = Math.min(eRes, aa_annotations.length);

    int x = 0, y2 = y;

    g.setColor(Color.pink);

    g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);

    int column;
    int aaMax = aa_annotations.length - 1;
    while (x < eRes - sRes)
    {
      column = sRes + x;
      if (hasHiddenColumns)
      {
        column = hiddenColumns.visibleToAbsoluteColumn(column);
      }
      // TODO: highlight columns selected
      boolean colsel = false;
      if (columnSelection != null)
      {
        colsel = columnSelection.contains(column);
      }

      if (column > aaMax)
      {
        break;
      }

      if (aa_annotations[column] == null)
      {
        x++;
        continue;
      }
      ContactListI contacts = viewport.getContactList(_aa, column);
      if (contacts == null)
      {
        x++;
        continue;
      }
      // Bean holding mapping from contact list to pixels
      final ContactGeometry cgeom = new ContactGeometry(contacts,
              _aa.graphHeight);

      for (int ht = y2, eht = y2
              - _aa.graphHeight; ht >= eht; ht -= cgeom.pixels_step)
      {
        ContactGeometry.contactInterval ci = cgeom.mapFor(y2 - ht,
                y2 - ht + cgeom.pixels_step);
        // cstart = (int) Math.floor(((double) y2 - ht) * contacts_per_pixel);
        // cend = (int) Math.min(contact_height,
        // Math.ceil(cstart + contacts_per_pixel * pixels_step));

        // TODO show maximum colour for range - sort of done
        // also need a 'getMaxPosForRange(start,end)' to accurately render
        Color col;
        boolean rowsel = false;
        if (columnSelection != null)
        {
          if (_aa.sequenceRef == null)
          {
            rowsel = columnSelection.intersects(ci.cStart, ci.cEnd);
          }
          else
          {
            // TODO check we have correctly mapped cstart to local sequence
            // numbering
            int s = _aa.sequenceRef.findIndex(ci.cStart);
            int e = _aa.sequenceRef.findIndex(ci.cEnd);
            if (s > 0 && s < _aa.sequenceRef.getLength())
            {
              rowsel = columnSelection.intersects(s, e);
            }
          }
        }
        // TODO: show selected region
        if (colsel || rowsel)
        {

          col = getSelectedColorForRange(min, max, contacts, ci.cStart,
                  ci.cEnd);
          if (colsel && rowsel)
          {
            col = new Color(col.getBlue(), col.getGreen(), col.getRed());
          }
          else
          {
            col = new Color(col.getBlue(), col.getBlue(), col.getBlue());
          }
          g.setColor(col);
        }
        else
        {
          col = getColorForRange(min, max, contacts, ci.cStart, ci.cEnd);
          g.setColor(col);
        }
        if (cgeom.pixels_step > 1)
        {
          g.fillRect(x * charWidth, ht, charWidth, 1 + cgeom.pixels_step);
        }
        else
        {
          g.drawLine(x * charWidth, ht, (x + 1) * charWidth, ht);
        }
      }
      x++;
    }

  }

  // Shading parameters
  // currently hardwired for alphafold
  Color maxColor = new Color(246, 252, 243),
          minColor = new Color(0, 60, 26),
          selMinColor = new Color(26, 0, 60),
          selMaxColor = new Color(243, 246, 252);

  Color shadeFor(float min, float max, float value)
  {
    return jalview.util.ColorUtils.getGraduatedColour(value, 0, minColor,
            max, maxColor);
  }

  public Color getColorForRange(float min, float max, ContactListI cl,
          int i, int j)
  {
    ContactRange cr = cl.getRangeFor(i, j);
    // average for moment - probably more interested in maxIntProj though
    return shadeFor(min, max, (float) cr.getMean());
  }

  public Color getSelectedColorForRange(float min, float max,
          ContactListI cl, int i, int j)
  {
    ContactRange cr = cl.getRangeFor(i, j);
    // average for moment - probably more interested in maxIntProj though
    return jalview.util.ColorUtils.getGraduatedColour((float) cr.getMean(),
            0, selMinColor, max, selMaxColor);
  }

}