/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
 * Copyright (C) 2015 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 java.awt.Color;

/**
 * ColourSchemeProperty binds names to hardwired colourschemes and tries to deal
 * intelligently with mapping unknown names to user defined colourschemes (that
 * exist or can be created from the string representation of the colourscheme
 * name - either a hex RGB triplet or a named colour under java.awt.color ). The
 * values of the colourscheme constants is important for callers of
 * getColourName(int i), since it can be used to enumerate the set of built in
 * colours. The FIRST_COLOUR and LAST_COLOUR symbols are provided for this.
 * 
 * @author $author$
 * @version $Revision$
 */
public class ColourSchemeProperty
{
  /** Undefined Colourscheme Index */
  public static final int UNDEFINED = -1;

  /** for schemes defined on the fly */
  public static final int USER_DEFINED = 0;

  /** No Colourscheme Index */
  public static final int NONE = 1;

  /** DOCUMENT ME!! */
  public static final int CLUSTAL = 2;

  /** DOCUMENT ME!! */
  public static final int BLOSUM = 3;

  /** DOCUMENT ME!! */
  public static final int PID = 4;

  /** DOCUMENT ME!! */
  public static final int ZAPPO = 5;

  /** DOCUMENT ME!! */
  public static final int TAYLOR = 6;

  /** DOCUMENT ME!! */
  public static final int HYDROPHOBIC = 7;

  /** DOCUMENT ME!! */
  public static final int HELIX = 8;

  /** DOCUMENT ME!! */
  public static final int STRAND = 9;

  /** DOCUMENT ME!! */
  public static final int TURN = 10;

  /** DOCUMENT ME!! */
  public static final int BURIED = 11;

  /** DOCUMENT ME!! */
  public static final int NUCLEOTIDE = 12;

  /**
   * purine/pyrimidine
   */
  public static final int PURINEPYRIMIDINE = 13;

  public static final int COVARIATION = 14;

  public static final int TCOFFEE = 15;

  public static final int RNAHELIX = 16;

  public static final int RNAINTERACTION = 17;

  /**
   * index of first colourscheme (includes 'None')
   */
  public static final int FIRST_COLOUR = NONE;

  public static final int LAST_COLOUR = RNAINTERACTION;

  /**
   * DOCUMENT ME!
   * 
   * @param name
   *          DOCUMENT ME!
   * 
   * @return DOCUMENT ME!
   */
  public static int getColourIndexFromName(String name)
  {
    int ret = UNDEFINED;

    if (name.equalsIgnoreCase("Clustal"))
    {
      ret = CLUSTAL;
    }
    else if (name.equalsIgnoreCase("Blosum62"))
    {
      ret = BLOSUM;
    }
    else if (name.equalsIgnoreCase("% Identity"))
    {
      ret = PID;
    }
    else if (name.equalsIgnoreCase("Zappo"))
    {
      ret = ZAPPO;
    }
    else if (name.equalsIgnoreCase("Taylor"))
    {
      ret = TAYLOR;
    }
    else if (name.equalsIgnoreCase("Hydrophobic"))
    {
      ret = HYDROPHOBIC;
    }
    else if (name.equalsIgnoreCase("Helix Propensity"))
    {
      ret = HELIX;
    }
    else if (name.equalsIgnoreCase("Strand Propensity"))
    {
      ret = STRAND;
    }
    else if (name.equalsIgnoreCase("Turn Propensity"))
    {
      ret = TURN;
    }
    else if (name.equalsIgnoreCase("Buried Index"))
    {
      ret = BURIED;
    }
    else if (name.equalsIgnoreCase("Nucleotide"))
    {
      ret = NUCLEOTIDE;
    }
    else if (name.equalsIgnoreCase("T-Coffee Scores"))
    {
      ret = TCOFFEE;
    }

    else if (name.equalsIgnoreCase("User Defined"))
    {
      ret = USER_DEFINED;
    }
    else if (name.equalsIgnoreCase("None"))
    {
      ret = NONE;
    }
    else if (name.equalsIgnoreCase("Purine/Pyrimidine"))
    {
      ret = PURINEPYRIMIDINE;
    }
    else if (name.equalsIgnoreCase("RNA Interaction type"))
    {
      ret = RNAINTERACTION;
    }
    else if (name.equalsIgnoreCase("RNA Helices"))
    {
      ret = RNAHELIX;
    }
    // else if (name.equalsIgnoreCase("Covariation"))
    // {
    // ret = COVARIATION;
    // }

    return ret;
  }

  /**
   * DOCUMENT ME!
   * 
   * @param cs
   *          DOCUMENT ME!
   * 
   * @return DOCUMENT ME!
   */
  public static String getColourName(ColourSchemeI cs)
  {

    int index = NONE;

    if (cs instanceof ClustalxColourScheme)
    {
      index = CLUSTAL;
    }
    else if (cs instanceof Blosum62ColourScheme)
    {
      index = BLOSUM;
    }
    else if (cs instanceof PIDColourScheme)
    {
      index = PID;
    }
    else if (cs instanceof ZappoColourScheme)
    {
      index = ZAPPO;
    }
    else if (cs instanceof TaylorColourScheme)
    {
      index = TAYLOR;
    }
    else if (cs instanceof HydrophobicColourScheme)
    {
      index = HYDROPHOBIC;
    }
    else if (cs instanceof HelixColourScheme)
    {
      index = HELIX;
    }
    else if (cs instanceof StrandColourScheme)
    {
      index = STRAND;
    }
    else if (cs instanceof TurnColourScheme)
    {
      index = TURN;
    }
    else if (cs instanceof BuriedColourScheme)
    {
      index = BURIED;
    }
    else if (cs instanceof NucleotideColourScheme)
    {
      index = NUCLEOTIDE;
    }
    else if (cs instanceof PurinePyrimidineColourScheme)
    {
      index = PURINEPYRIMIDINE;
    }
    else if (cs instanceof TCoffeeColourScheme)
    {
      index = TCOFFEE;
    }
    else if (cs instanceof RNAHelicesColour)
    {
      index = RNAHELIX;
    }
    /*
     * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
     */
    else if (cs instanceof UserColourScheme)
    {
      if ((((UserColourScheme) cs).getName() != null)
              && (((UserColourScheme) cs).getName().length() > 0))
      {
        return ((UserColourScheme) cs).getName();
      }
      // get default colourscheme name
      index = USER_DEFINED;
    }

    return getColourName(index);
  }

  /**
   * DOCUMENT ME!
   * 
   * @param index
   *          DOCUMENT ME!
   * 
   * @return DOCUMENT ME!
   */
  public static String getColourName(int index)
  {
    String ret = null;

    switch (index)
    {
    case CLUSTAL:
      ret = "Clustal";

      break;

    case BLOSUM:
      ret = "Blosum62";

      break;

    case PID:
      ret = "% Identity";

      break;

    case ZAPPO:
      ret = "Zappo";

      break;

    case TAYLOR:
      ret = "Taylor";
      break;

    case HYDROPHOBIC:
      ret = "Hydrophobic";

      break;

    case HELIX:
      ret = "Helix Propensity";

      break;

    case STRAND:
      ret = "Strand Propensity";

      break;

    case TURN:
      ret = "Turn Propensity";

      break;

    case BURIED:
      ret = "Buried Index";

      break;

    case NUCLEOTIDE:
      ret = "Nucleotide";

      break;

    case PURINEPYRIMIDINE:
      ret = "Purine/Pyrimidine";

      break;

    case TCOFFEE:
      ret = "T-Coffee Scores";

      break;

    case RNAINTERACTION:
      ret = "RNA Interaction type";

      break;
    case RNAHELIX:
      ret = "RNA Helices";

      break;
    /*
     * case COVARIATION: ret = "Covariation";
     * 
     * break;
     */
    case USER_DEFINED:
      ret = "User Defined";

      break;

    default:
      ret = "None";

      break;
    }

    return ret;
  }

  /**
   * retrieve or create colourscheme associated with name
   * 
   * @param seqs
   *          sequences to colour
   * @param width
   *          range of sequences to colour
   * @param name
   *          colourscheme name, applet colour parameter specification, or
   *          string to parse as colour for new coloursheme
   * @return Valid Colourscheme
   */
  public static ColourSchemeI getColour(AnnotatedCollectionI alignment,
          String name)
  {
    int colindex = getColourIndexFromName(name);
    if (colindex == UNDEFINED)
    {
      if (name.indexOf('=') == -1)
      {
        // try to build a colour from the string directly
        try
        {
          return new UserColourScheme(name);
        } catch (Exception e)
        {
          // System.err.println("Ignoring unknown colourscheme name");
        }
      }
      else
      {
        // try to parse the string as a residue colourscheme
        try
        {
          // fix the launchApp user defined coloursheme transfer bug
          jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
                  "white");
          ucs.parseAppletParameter(name);

        } catch (Exception e)
        {
          // System.err.println("Ignoring exception when parsing colourscheme as applet-parameter");
        }
      }
    }
    return getColour(alignment, getColourIndexFromName(name));
  }

  /**
   * Construct an instance of ColourSchemeI corresponding to the given
   * colourscheme index
   * 
   * @param seqs
   *          sequences to be coloured by colourscheme
   * @param width
   *          geometry of alignment
   * @param index
   *          colourscheme number
   * 
   * @return null or an instance of the colourscheme configured to colour given
   *         sequence set
   */
  public static ColourSchemeI getColour(
          jalview.datamodel.AnnotatedCollectionI coll, int index)
  {
    // TODO 3.0 2.8 refactor signature to take an alignmentI like container so
    // colourschemes based on annotation can be initialised
    ColourSchemeI cs = null;

    switch (index)
    {
    case CLUSTAL:
      cs = new ClustalxColourScheme(coll, null);

      break;

    case BLOSUM:
      cs = new Blosum62ColourScheme();

      break;

    case PID:
      cs = new PIDColourScheme();

      break;

    case ZAPPO:
      cs = new ZappoColourScheme();

      break;

    case TAYLOR:
      cs = new TaylorColourScheme();
      break;

    case HYDROPHOBIC:
      cs = new HydrophobicColourScheme();

      break;

    case HELIX:
      cs = new HelixColourScheme();

      break;

    case STRAND:
      cs = new StrandColourScheme();

      break;

    case TURN:
      cs = new TurnColourScheme();

      break;

    case BURIED:
      cs = new BuriedColourScheme();

      break;

    case NUCLEOTIDE:
      cs = new NucleotideColourScheme();

      break;

    case PURINEPYRIMIDINE:
      cs = new PurinePyrimidineColourScheme();

      break;

    case TCOFFEE:
      cs = new TCoffeeColourScheme(coll);
      break;

    case RNAHELIX:
      cs = new RNAHelicesColour(coll);
      break;

    // case COVARIATION:
    // cs = new CovariationColourScheme(annotation);
    // break;

    case USER_DEFINED:
      Color[] col = new Color[24];
      for (int i = 0; i < 24; i++)
      {
        col[i] = Color.white;
      }
      cs = new UserColourScheme(col);
      break;

    default:
      break;
    }

    return cs;
  }

  public static Color getAWTColorFromName(String name)
  {
    Color col = null;
    name = name.toLowerCase();
    if (name.equals("black"))
    {
      col = Color.black;
    }
    else if (name.equals("blue"))
    {
      col = Color.blue;
    }
    else if (name.equals("cyan"))
    {
      col = Color.cyan;
    }
    else if (name.equals("darkGray"))
    {
      col = Color.darkGray;
    }
    else if (name.equals("gray"))
    {
      col = Color.gray;
    }
    else if (name.equals("green"))
    {
      col = Color.green;
    }
    else if (name.equals("lightGray"))
    {
      col = Color.lightGray;
    }
    else if (name.equals("magenta"))
    {
      col = Color.magenta;
    }
    else if (name.equals("orange"))
    {
      col = Color.orange;
    }
    else if (name.equals("pink"))
    {
      col = Color.pink;
    }
    else if (name.equals("red"))
    {
      col = Color.red;
    }
    else if (name.equals("white"))
    {
      col = Color.white;
    }
    else if (name.equals("yellow"))
    {
      col = Color.yellow;
    }

    return col;
  }

  public static Color rnaHelices[] = null;

  public static void initRnaHelicesShading(int n)
  {
    int j = 0;
    if (rnaHelices == null)
    {
      rnaHelices = new Color[n + 1];
    }
    else if (rnaHelices != null && rnaHelices.length <= n)
    {
      Color[] t = new Color[n + 1];
      System.arraycopy(rnaHelices, 0, t, 0, rnaHelices.length);
      j = rnaHelices.length;
      rnaHelices = t;
    }
    else
    {
      return;
    }
    // Generate random colors and store
    for (; j <= n; j++)
    {
      rnaHelices[j] = jalview.util.ColorUtils
              .generateRandomColor(Color.white);
    }
  }

  /**
   * delete the existing cached RNA helces colours
   */
  public static void resetRnaHelicesShading()
  {
    rnaHelices = null;
  }

}