/*
 * 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.renderer;

import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.util.Comparison;

import java.awt.Color;

public class OverviewResColourFinder extends ResidueColourFinder
{
  final int GAP_COLOUR; // default colour to use at gaps

  final int RESIDUE_COLOUR; // default colour to use at residues

  final Color HIDDEN_COLOUR; // colour for hidden regions

  boolean useLegacy = false;

  public static final Color OVERVIEW_DEFAULT_GAP = Color.lightGray;

  public static final Color OVERVIEW_DEFAULT_LEGACY_GAP = Color.white;

  public static final Color OVERVIEW_DEFAULT_HIDDEN = Color.darkGray
          .darker();

  /**
   * Constructor without colour settings (used by applet)
   */
  public OverviewResColourFinder()
  {
    this(false, OVERVIEW_DEFAULT_GAP, OVERVIEW_DEFAULT_HIDDEN);
  }

  /**
   * Constructor with colour settings
   * 
   * @param useLegacyColouring
   *          whether to use legacy gap colouring (white gaps, grey residues)
   * @param gapCol
   *          gap colour if not legacy
   * @param hiddenCol
   *          hidden region colour (transparency applied by rendering code)
   */
  public OverviewResColourFinder(boolean useLegacyColouring, Color gapCol,
          Color hiddenCol)
  {
    if (useLegacyColouring)
    {
      GAP_COLOUR = Color.white.getRGB();
      RESIDUE_COLOUR = Color.lightGray.getRGB();
    }
    else
    {
      GAP_COLOUR = gapCol.getRGB();
      RESIDUE_COLOUR = Color.white.getRGB();
    }
    HIDDEN_COLOUR = hiddenCol;
  }

  @Override
  /**
   * for Test suite only.
   */
  public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
  {
    return new Color(getBoxColourInt(shader, seq, i));
  }

  public int getBoxColourInt(ResidueShaderI shader, SequenceI seq, int i)
  {
    char currentChar = seq.getCharAt(i);
    // In the overview window, gaps are coloured grey, unless the colour scheme
    // specifies a gap colour, in which case gaps honour the colour scheme
    // settings
    boolean isGap = Comparison.isGap(currentChar);
    if (shader.getColourScheme() == null)
    {
      return (isGap ? GAP_COLOUR : RESIDUE_COLOUR);
    }
    return (isGap && !shader.getColourScheme().hasGapColour() ? GAP_COLOUR
            : shader.findColourInt(currentChar, i, seq));
  }

  /**
   * For test suite only.
   */
  @Override
  public Color getResidueColour(boolean showBoxes, ResidueShaderI shader,
          SequenceGroup[] allGroups, final SequenceI seq, int i,
          FeatureColourFinder finder)
  {
    return new Color(getResidueColourInt(showBoxes, shader, allGroups, seq,
            i, finder));
  }


  public int getResidueColourInt(boolean showBoxes, ResidueShaderI shader,
          SequenceGroup[] allGroups, final SequenceI seq, int i,
          FeatureColourFinder finder)
  {

    int c = seq.getColor(i);
    if (c != 0)
    {
      return c;
    }

    int col = getResidueBoxColourInt(showBoxes, shader, allGroups, seq, i);

    // if there's a FeatureColourFinder we might override the residue colour
    // here with feature colouring
    return seq.setColor(i,
            finder == null || finder.noFeaturesDisplayed() ? col
                    : finder.findFeatureColourInt(col, seq, i));
  }

  /**
   * For test suite only.
   */
  @Override
  protected Color getResidueBoxColour(boolean showBoxes,
          ResidueShaderI shader, SequenceGroup[] allGroups, SequenceI seq,
          int i)
  {
    return new Color(
            getResidueBoxColourInt(showBoxes, shader, allGroups, seq, i));
  }

  /**
   * In the overview, the showBoxes setting is ignored, as the overview displays
   * the colours regardless.
   */
  protected int getResidueBoxColourInt(boolean showBoxes,
          ResidueShaderI shader, SequenceGroup[] allGroups, SequenceI seq,
          int i)
  {
    SequenceGroup currentSequenceGroup = getCurrentSequenceGroup(allGroups,
            i);
    ResidueShaderI currentShader = (currentSequenceGroup == null ? shader
            : currentSequenceGroup.getGroupColourScheme());
    return getBoxColourInt(currentShader, seq, i);
  }

  /**
   * Supply hidden colour
   * 
   * @return colour of hidden regions
   */
  protected Color getHiddenColour()
  {
    return HIDDEN_COLOUR;
  }
}