/*
 * 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.schemes;

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

import java.awt.Color;
import java.util.Map;
import java.util.StringTokenizer;

public class UserColourScheme extends ResidueColourScheme
{
  Color[] lowerCaseColours;

  protected String schemeName;

  public UserColourScheme()
  {
    super(ResidueProperties.aaIndex);
  }

  public UserColourScheme(Color[] newColors)
  {
    super(ResidueProperties.aaIndex);
    colors = newColors;
  }

  @Override
  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
  {
    UserColourScheme usc = new UserColourScheme(colors);
    if (lowerCaseColours != null)
    {
      usc.schemeName = new String(schemeName);
      usc.lowerCaseColours = new Color[lowerCaseColours.length];
      System.arraycopy(lowerCaseColours, 0, usc.lowerCaseColours, 0,
              lowerCaseColours.length);
    }
    return usc;
  }

  public UserColourScheme(String colour)
  {
    super(ResidueProperties.aaIndex);
    Color col = ColorUtils.parseColourString(colour);

    if (col == null)
    {
      System.out.println("Making colour from name: " + colour);
      col = ColorUtils.createColourFromName(colour);
    }

    colors = new Color[24];
    for (int i = 0; i < 24; i++)
    {
      colors[i] = col;
    }
    schemeName = colour;
  }

  public Color[] getColours()
  {
    return colors;
  }

  public Color[] getLowerCaseColours()
  {
    return lowerCaseColours;
  }

  public void setName(String name)
  {
    schemeName = name;
  }

  public String getName()
  {
    return schemeName;
  }

  /**
   * Parse and save residue colours specified as (for example)
   * 
   * <pre>
   *     D,E=red; K,R,H=0022FF; c=100,50,75
   * </pre>
   * 
   * This should be a semi-colon separated list of colours, which may be defined
   * by colour name, hex value or comma-separated RGB triple. Each colour is
   * defined for a comma-separated list of amino acid single letter codes. (Note
   * that this also allows a colour scheme to be defined for ACGT, but not for
   * U.)
   * 
   * @param paramValue
   */
  public void parseAppletParameter(String paramValue)
  {
    // TODO: need a function to generate appletParameter colour string from a
    // UCS
    StringTokenizer st = new StringTokenizer(paramValue, ";");
    StringTokenizer st2;
    String token = null, colour, residues;
    try
    {
      while (st.hasMoreElements())
      {
        token = st.nextToken().trim();
        residues = token.substring(0, token.indexOf("="));
        colour = token.substring(token.indexOf("=") + 1);

        st2 = new StringTokenizer(residues, " ,");
        while (st2.hasMoreTokens())
        {
          String residue = st2.nextToken();

          int colIndex = ResidueProperties.aaIndex[residue.charAt(0)];
          if (colIndex == -1)
          {
            continue;
          }

          if (residue.equalsIgnoreCase("lowerCase"))
          {
            if (lowerCaseColours == null)
            {
              lowerCaseColours = new Color[23];
            }
            for (int i = 0; i < 23; i++)
            {
              if (lowerCaseColours[i] == null)
              {
                lowerCaseColours[i] = ColorUtils.parseColourString(colour);
              }
            }

            continue;
          }

          if (residue.equals(residue.toLowerCase()))
          {
            if (lowerCaseColours == null)
            {
              lowerCaseColours = new Color[23];
            }
            lowerCaseColours[colIndex] = ColorUtils.parseColourString(colour);
          }
          else
          {
            colors[colIndex] = ColorUtils.parseColourString(colour);
          }
        }
      }
    } catch (Exception ex)
    {
      System.out.println("Error parsing userDefinedColours:\n" + token
              + "\n" + ex);
    }

  }

  @Override
  public Color findColour(char c, int j, SequenceI seq)
  {
    Color currentColour;
    int index = ResidueProperties.aaIndex[c];

    if ((threshold == 0) || aboveThreshold(c, j))
    {
      if (lowerCaseColours != null && 'a' <= c && c <= 'z')
      {
        currentColour = lowerCaseColours[index];
      }
      else
      {
        currentColour = colors[index];
      }
    }
    else
    {
      currentColour = Color.white;
    }

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

    return currentColour;
  }

  public void setLowerCaseColours(Color[] lcolours)
  {
    lowerCaseColours = lcolours;
  }

  /**
   * Returns the colour for the given residue character. If the residue is
   * lower-case, and there is a specific colour defined for lower case, that
   * colour is returned, else the colour for the upper case residue.
   */
  @Override
  public Color findColour(char c)
  {
    if ('a' <= c && c <= 'z' && lowerCaseColours != null)
    {
      Color colour = lowerCaseColours[symbolIndex[c]];
      if (colour != null)
      {
        return colour;
      }
    }
    return super.findColour(c);
  }

  /**
   * Answers the customised name of the colour scheme, if it has one, else
   * "User Defined"
   */
  @Override
  public String getSchemeName()
  {
    if (schemeName != null && schemeName.length() > 0)
    {
      return schemeName;
    }
    return JalviewColourScheme.UserDefined.toString();
  }

}