/*
 * 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.ext.rbvi.chimera;

import jalview.structure.AtomSpecModel;
import jalview.util.ColorUtils;
import jalview.util.IntRangeComparator;

import java.awt.Color;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;

/**
 * Routines for generating ChimeraX commands for Jalview/ChimeraX binding
 */
public class ChimeraXCommands extends ChimeraCommands
{
  private static final String CMD_COLOUR_BY_CHARGE = "color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow";

  @Override
  public String colourByCharge()
  {
    return CMD_COLOUR_BY_CHARGE;
  }

  @Override
  public String getResidueSpec(String residue)
  {
    return ":" + residue;
  }

  @Override
  public String setBackgroundColour(Color col)
  {
    // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/set.html
    return "set bgColor " + ColorUtils.toTkCode(col);
  }

  @Override
  protected String getColourCommand(AtomSpecModel colourData,
          Color colour)
  {
    // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html
    String colourCode = getColourString(colour);

    return "color " + getAtomSpec(colourData, false) + " " + colourCode;
  }

  @Override
  public String focusView()
  {
    // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/view.html
    return "view";
  }

  /**
   * {@inheritDoc}
   * 
   * @return
   */
  @Override
  public int getModelStartNo()
  {
    return 1;
  }

  /**
   * Returns a viewer command to set the given residue attribute value on
   * residues specified by the AtomSpecModel, for example
   * 
   * <pre>
   * setattr #0/A:3-9,14-20,39-43 res jv_strand 'strand' create true
   * </pre>
   * 
   * @param attributeName
   * @param attributeValue
   * @param atomSpecModel
   * @return
   */
  @Override
  protected String getSetAttributeCommand(String attributeName,
          String attributeValue, AtomSpecModel atomSpecModel)
  {
    StringBuilder sb = new StringBuilder(128);
    sb.append("setattr ").append(getAtomSpec(atomSpecModel, false));
    sb.append(" res ").append(attributeName).append(" '")
            .append(attributeValue).append("'");
    sb.append(" create true");
    return sb.toString();
  }

  @Override
  public String openCommandFile(String path)
  {
    // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html
    return "open " + path;
  }

  @Override
  public String saveSession(String filepath)
  {
    // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html
    return "save session " + filepath;
  }

  /**
   * Returns the range(s) formatted as a ChimeraX atomspec, for example
   * <p>
   * #1/A:2-20,30-40/B:10-20|#2/A:12-30
   * 
   * @return
   */
  @Override
  public String getAtomSpec(AtomSpecModel atomSpec, boolean alphaOnly)
  {
    StringBuilder sb = new StringBuilder(128);
    boolean firstModel = true;
    for (Integer model : atomSpec.getModels())
    {
      if (!firstModel)
      {
        sb.append("|");
      }
      firstModel = false;
      appendModel(sb, model, atomSpec);
      if (alphaOnly)
      {
        sb.append("@CA|P");
      }
      // todo: is there ChimeraX syntax to exclude altlocs?
    }
    return sb.toString();
  }

  /**
   * A helper method to append an atomSpec string for atoms in the given model
   * 
   * @param sb
   * @param model
   * @param atomSpec
   */
  protected void appendModel(StringBuilder sb, Integer model,
          AtomSpecModel atomSpec)
  {
    sb.append("#").append(model);

    for (String chain : atomSpec.getChains(model))
    {
      boolean firstPositionForChain = true;
      chain = " ".equals(chain) ? chain : chain.trim();
      sb.append("/").append(chain).append(":");
      List<int[]> rangeList = atomSpec.getRanges(model, chain);

      /*
       * sort ranges into ascending start position order
       */
      Collections.sort(rangeList, IntRangeComparator.ASCENDING);

      int start = rangeList.isEmpty() ? 0 : rangeList.get(0)[0];
      int end = rangeList.isEmpty() ? 0 : rangeList.get(0)[1];

      Iterator<int[]> iterator = rangeList.iterator();
      while (iterator.hasNext())
      {
        int[] range = iterator.next();
        if (range[0] <= end + 1)
        {
          /*
           * range overlaps or is contiguous with the last one
           * - so just extend the end position, and carry on
           * (unless this is the last in the list)
           */
          end = Math.max(end, range[1]);
        }
        else
        {
          /*
           * we have a break so append the last range
           */
          appendRange(sb, start, end, chain, firstPositionForChain, true);
          start = range[0];
          end = range[1];
          firstPositionForChain = false;
        }
      }

      /*
       * and append the last range
       */
      if (!rangeList.isEmpty())
      {
        appendRange(sb, start, end, chain, firstPositionForChain, true);
      }
      firstPositionForChain = false;
    }
  }

  @Override
  public String showBackbone()
  {
    return "~display all;show @CA|P pbonds";
  }

  @Override
  public String superposeStructures(AtomSpecModel spec, AtomSpecModel ref)
  {
    /*
     * Form ChimeraX match command to match spec to ref
     * 
     * match #1/A:2-94 toAtoms #2/A:1-93
     * 
     * @see
     * https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
     */
    StringBuilder cmd = new StringBuilder();
    String atomSpec = getAtomSpec(spec, true);
    String refSpec = getAtomSpec(ref, true);
    cmd.append("align ").append(atomSpec).append(" toAtoms ")
            .append(refSpec);

    /*
     * show superposed residues as ribbon, others as chain
     */
    cmd.append("; ribbon ");
    cmd.append(getAtomSpec(spec, false)).append("|");
    cmd.append(getAtomSpec(ref, false)).append("; view");

    return cmd.toString();
  }

}