/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
 * Copyright (C) 2014 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.schemes;

import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;

import java.awt.Color;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
import java.util.Vector;

public class ClustalxColourScheme extends ResidueColourScheme // implements
// IParameterizable
{
  public static Hashtable colhash = new Hashtable();

  Hashtable[] cons;

  int[][] cons2;

  ConsensusColour[] colours;

  ConsensusColour[] ResidueColour;

  int size;

  Consensus[] conses = new Consensus[32];

  Vector colourTable = new Vector();

  private boolean includeGaps = true;

  {
    colhash.put("RED", new Color((float) 0.9, (float) 0.2, (float) 0.1));
    colhash.put("BLUE", new Color((float) 0.5, (float) 0.7, (float) 0.9));
    colhash.put("GREEN", new Color((float) 0.1, (float) 0.8, (float) 0.1));
    colhash.put("ORANGE", new Color((float) 0.9, (float) 0.6, (float) 0.3));
    colhash.put("CYAN", new Color((float) 0.1, (float) 0.7, (float) 0.7));
    colhash.put("PINK", new Color((float) 0.9, (float) 0.5, (float) 0.5));
    colhash.put("MAGENTA", new Color((float) 0.8, (float) 0.3, (float) 0.8));
    colhash.put("YELLOW", new Color((float) 0.8, (float) 0.8, (float) 0.0));
  }

  public ClustalxColourScheme(AnnotatedCollectionI alignment,
          Map<SequenceI, SequenceCollectionI> hiddenReps)
  {
    alignmentChanged(alignment, hiddenReps);
  }

  public void alignmentChanged(AnnotatedCollectionI alignment,
          Map<SequenceI, SequenceCollectionI> hiddenReps)
  {
    int maxWidth = alignment.getWidth();
    List<SequenceI> seqs = alignment.getSequences(hiddenReps);
    cons2 = new int[maxWidth][24];
    includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
    // get the current setting of the
    // includeGaps param.
    int start = 0;

    // Initialize the array
    for (int j = 0; j < 24; j++)
    {
      for (int i = 0; i < maxWidth; i++)
      {
        cons2[i][j] = 0;
      }
    }

    int res;
    int i;
    int j = 0;
    char[] seq;

    for (SequenceI sq : seqs)
    {
      seq = sq.getSequence();

      int end_j = seq.length - 1;

      for (i = start; i <= end_j; i++)
      {
        if ((seq.length - 1) < i)
        {
          res = 23;
        }
        else
        {
          res = ResidueProperties.aaIndex[seq[i]];
        }

        cons2[i][res]++;
      }

      j++;
    }

    this.size = seqs.size();
    makeColours();
  }

  public void makeColours()
  {
    conses[0] = new Consensus("WLVIMAFCYHP", 60);
    conses[1] = new Consensus("WLVIMAFCYHP", 80);
    conses[2] = new Consensus("ED", 50);
    conses[3] = new Consensus("KR", 60);
    conses[4] = new Consensus("G", 50);
    conses[5] = new Consensus("N", 50);
    conses[6] = new Consensus("QE", 50);
    conses[7] = new Consensus("P", 50);
    conses[8] = new Consensus("TS", 50);

    conses[26] = new Consensus("A", 85);
    conses[27] = new Consensus("C", 85);
    conses[10] = new Consensus("E", 85);
    conses[11] = new Consensus("F", 85);
    conses[12] = new Consensus("G", 85);
    conses[13] = new Consensus("H", 85);
    conses[14] = new Consensus("I", 85);
    conses[15] = new Consensus("L", 85);
    conses[16] = new Consensus("M", 85);
    conses[17] = new Consensus("N", 85);
    conses[18] = new Consensus("P", 85);
    conses[19] = new Consensus("Q", 85);
    conses[20] = new Consensus("R", 85);
    conses[21] = new Consensus("S", 85);
    conses[22] = new Consensus("T", 85);
    conses[23] = new Consensus("V", 85);
    conses[24] = new Consensus("W", 85);
    conses[25] = new Consensus("Y", 85);
    conses[28] = new Consensus("K", 85);
    conses[29] = new Consensus("D", 85);

    conses[30] = new Consensus("G", 0);
    conses[31] = new Consensus("P", 0);

    // We now construct the colours
    colours = new ConsensusColour[11];

    Consensus[] tmp8 = new Consensus[1];
    tmp8[0] = conses[30]; // G
    colours[7] = new ConsensusColour((Color) colhash.get("ORANGE"), tmp8);

    Consensus[] tmp9 = new Consensus[1];
    tmp9[0] = conses[31]; // P
    colours[8] = new ConsensusColour((Color) colhash.get("YELLOW"), tmp9);

    Consensus[] tmp10 = new Consensus[1];
    tmp10[0] = conses[27]; // C
    colours[9] = new ConsensusColour((Color) colhash.get("PINK"), tmp8);

    Consensus[] tmp1 = new Consensus[14];
    tmp1[0] = conses[0]; // %
    tmp1[1] = conses[1]; // #
    tmp1[2] = conses[26]; // A
    tmp1[3] = conses[27]; // C
    tmp1[4] = conses[11]; // F
    tmp1[5] = conses[13]; // H
    tmp1[6] = conses[14]; // I
    tmp1[7] = conses[15]; // L
    tmp1[8] = conses[16]; // M
    tmp1[9] = conses[23]; // V
    tmp1[10] = conses[24]; // W
    tmp1[11] = conses[25]; // Y
    tmp1[12] = conses[18]; // P
    tmp1[13] = conses[19]; // p
    colours[0] = new ConsensusColour((Color) colhash.get("BLUE"), tmp1);

    colours[10] = new ConsensusColour((Color) colhash.get("CYAN"), tmp1);

    Consensus[] tmp2 = new Consensus[5];
    tmp2[0] = conses[8]; // t
    tmp2[1] = conses[21]; // S
    tmp2[2] = conses[22]; // T
    tmp2[3] = conses[0]; // %
    tmp2[4] = conses[1]; // #
    colours[1] = new ConsensusColour((Color) colhash.get("GREEN"), tmp2);

    Consensus[] tmp3 = new Consensus[3];

    tmp3[0] = conses[17]; // N
    tmp3[1] = conses[29]; // D
    tmp3[2] = conses[5]; // n
    colours[2] = new ConsensusColour((Color) colhash.get("GREEN"), tmp3);

    Consensus[] tmp4 = new Consensus[6];
    tmp4[0] = conses[6]; // q = QE
    tmp4[1] = conses[19]; // Q
    tmp4[2] = conses[22]; // E
    tmp4[3] = conses[3]; // +
    tmp4[4] = conses[28]; // K
    tmp4[5] = conses[20]; // R
    colours[3] = new ConsensusColour((Color) colhash.get("GREEN"), tmp4);

    Consensus[] tmp5 = new Consensus[4];
    tmp5[0] = conses[3]; // +
    tmp5[1] = conses[28]; // K
    tmp5[2] = conses[20]; // R
    tmp5[3] = conses[19]; // Q
    colours[4] = new ConsensusColour((Color) colhash.get("RED"), tmp5);

    Consensus[] tmp6 = new Consensus[6];
    tmp6[0] = conses[3]; // -
    tmp6[1] = conses[29]; // D
    tmp6[2] = conses[10]; // E
    tmp6[3] = conses[6]; // QE
    tmp6[4] = conses[19]; // Q
    tmp6[5] = conses[2]; // DE
    colours[5] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp6);

    Consensus[] tmp7 = new Consensus[5];
    tmp7[0] = conses[3]; // -
    tmp7[1] = conses[29]; // D
    tmp7[2] = conses[10]; // E
    tmp7[3] = conses[17]; // N
    tmp7[4] = conses[2]; // DE
    colours[6] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp7);

    // Now attach the ConsensusColours to the residue letters
    ResidueColour = new ConsensusColour[20];
    ResidueColour[0] = colours[0]; // A
    ResidueColour[1] = colours[4]; // R
    ResidueColour[2] = colours[2]; // N
    ResidueColour[3] = colours[6]; // D
    ResidueColour[4] = colours[0]; // C
    ResidueColour[5] = colours[3]; // Q
    ResidueColour[6] = colours[5]; // E
    ResidueColour[7] = colours[7]; // G
    ResidueColour[8] = colours[10]; // H
    ResidueColour[9] = colours[0]; // I
    ResidueColour[10] = colours[0]; // L
    ResidueColour[11] = colours[4]; // K
    ResidueColour[12] = colours[0]; // M
    ResidueColour[13] = colours[0]; // F
    ResidueColour[14] = colours[8]; // P
    ResidueColour[15] = colours[1]; // S
    ResidueColour[16] = colours[1]; // T
    ResidueColour[17] = colours[0]; // W
    ResidueColour[18] = colours[10]; // Y
    ResidueColour[19] = colours[0]; // V
  }

  @Override
  public Color findColour(char c)
  {
    return Color.pink;
  }

  @Override
  public Color findColour(char c, int j, SequenceI seq)
  {
    Color currentColour;

    if (cons2.length <= j
            || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
    {
      return Color.white;
    }

    int i = ResidueProperties.aaIndex[c];

    currentColour = Color.white;

    if (i > 19)
    {
      return currentColour;
    }

    for (int k = 0; k < ResidueColour[i].conses.length; k++)
    {
      if (ResidueColour[i].conses[k].isConserved(cons2, j, size,
              includeGaps))
      {
        currentColour = ResidueColour[i].c;
      }
    }

    if (i == 4)
    {
      if (conses[27].isConserved(cons2, j, size, includeGaps))
      {
        currentColour = (Color) colhash.get("PINK");
      }
    }

    if (conservationColouring)
    {
      currentColour = applyConservation(currentColour, j);
    }

    return currentColour;
  }

  /**
   * @return the includeGaps
   */
  protected boolean isIncludeGaps()
  {
    return includeGaps;
  }

  /**
   * @param includeGaps
   *          the includeGaps to set
   */
  protected void setIncludeGaps(boolean includeGaps)
  {
    this.includeGaps = includeGaps;
  }

  @Override
  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
  {
    ClustalxColourScheme css = new ClustalxColourScheme(sg,
            hiddenRepSequences);
    css.includeGaps = includeGaps;
    return css;
  }
}

class ConsensusColour
{
  Consensus[] conses;

  Color c;

  public ConsensusColour(Color c, Consensus[] conses)
  {
    this.conses = conses;

    // this.list = list;
    this.c = c;
  }
}