package jalview.ext.pymol;

import java.awt.Color;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;

import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsBase;

/**
 * A class that generates commands to send to PyMol over its XML-RPC interface.
 * <p>
 * Note that because the xml-rpc interface can only accept one command at a
 * time, we can't concatenate commands, and must instead form and send them
 * individually.
 * 
 * @see https://pymolwiki.org/index.php/Category:Commands
 * @see https://pymolwiki.org/index.php/RPC
 */
public class PymolCommands extends StructureCommandsBase
{
  private static final StructureCommand COLOUR_BY_CHAIN = new StructureCommand("spectrum", "chain");

  private static final List<StructureCommandI> COLOR_BY_CHARGE = new ArrayList<>();

  private static final List<StructureCommandI> SHOW_BACKBONE = new ArrayList<>();

  static {
    COLOR_BY_CHARGE.add(new StructureCommand("color", "white", "*"));
    COLOR_BY_CHARGE
            .add(new StructureCommand("color", "red", "resn ASP resn GLU"));
    COLOR_BY_CHARGE.add(
            new StructureCommand("color", "blue", "resn LYS resn ARG"));
    COLOR_BY_CHARGE
            .add(new StructureCommand("color", "yellow", "resn CYS"));
    SHOW_BACKBONE.add(new StructureCommand("hide", "everything"));
    SHOW_BACKBONE.add(new StructureCommand("show", "ribbon"));
  }

  @Override
  public StructureCommandI colourByChain()
  {
    return COLOUR_BY_CHAIN;
  }

  @Override
  public List<StructureCommandI> colourByCharge()
  {
    return COLOR_BY_CHARGE;
  }

  @Override
  public StructureCommandI setBackgroundColour(Color col)
  {
    // https://pymolwiki.org/index.php/Bg_Color
    return new StructureCommand("bg_color", getColourString(col));
  }

  /**
   * Returns a colour formatted suitable for use in viewer command syntax. For
   * example, red is {@code "0xff0000"}.
   * 
   * @param c
   * @return
   */
  protected String getColourString(Color c)
  {
    return String.format("0x%02x%02x%02x", c.getRed(), c.getGreen(),
            c.getBlue());
  }

  @Override
  public StructureCommandI focusView()
  {
    // TODO what?
    return null;
  }

  @Override
  public List<StructureCommandI> showChains(List<String> toShow)
  {
    // https://pymolwiki.org/index.php/Show
    List<StructureCommandI> commands = new ArrayList<>();
    commands.add(new StructureCommand("hide", "everything"));
    commands.add(new StructureCommand("show", "lines"));
    StringBuilder chains = new StringBuilder();
    for (String chain : toShow)
    {
      chains.append(" chain ").append(chain);
    }
    commands.add(new StructureCommand("show", "cartoon", chains.toString()));
    return commands;
  }

  @Override
  public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
          AtomSpecModel atomSpec)
  {
    // https://pymolwiki.org/index.php/Super
    List<StructureCommandI> commands = new ArrayList<>();
    String refAtomsAlphaOnly = getAtomSpec(refAtoms, true);
    String atomSpec2AlphaOnly = getAtomSpec(atomSpec, true);
    commands.add(new StructureCommand("super", refAtomsAlphaOnly,
            atomSpec2AlphaOnly));

    /*
     * and show superposed residues as cartoon
     */
    String refAtomsAll = getAtomSpec(refAtoms, false);
    String atomSpec2All = getAtomSpec(atomSpec, false);
    commands.add(new StructureCommand("show", "cartoon",
            refAtomsAll + " " + atomSpec2All));

    return commands;
  }

  @Override
  public StructureCommandI openCommandFile(String path)
  {
    // https://pymolwiki.org/index.php/Run
    return new StructureCommand("run", path); // should be .pml
  }

  @Override
  public StructureCommandI saveSession(String filepath)
  {
    // https://pymolwiki.org/index.php/Save#EXAMPLES
    return new StructureCommand("save", filepath); // should be .pse
  }

  /**
   * Returns a selection string in PyMOL 'selection macro' format:
   * 
   * <pre>
   * modelId// chain/residues/
   * </pre>
   * 
   * If more than one chain, makes a selection expression for each, and they are
   * separated by spaces.
   * 
   * @see https://pymolwiki.org/index.php/Selection_Macros
   */
  @Override
  public String getAtomSpec(AtomSpecModel model, boolean alphaOnly)
  {
    StringBuilder sb = new StringBuilder(64);
    boolean first = true;
    for (String modelId : model.getModels())
    {
      for (String chain : model.getChains(modelId))
      {
        if (!first)
        {
          sb.append(" ");
        }
        first = false;
        List<int[]> rangeList = model.getRanges(modelId, chain);
        chain = chain.trim();
        sb.append(modelId).append("//").append(chain).append("/");
        boolean firstRange = true;
        for (int[] range : rangeList)
        {
          if (!firstRange)
          {
            sb.append("+");
          }
          firstRange = false;
          sb.append(String.valueOf(range[0]));
          if (range[0] != range[1])
          {
            sb.append("-").append(String.valueOf(range[1]));
          }
        }
        sb.append("/");
        if (alphaOnly)
        {
          sb.append("CA");
        }
      }
    }
    return sb.toString();
  }

  @Override
  public List<StructureCommandI> showBackbone()
  {
    return SHOW_BACKBONE;
  }

  @Override
  protected StructureCommandI getColourCommand(String atomSpec, Color colour)
  {
    // https://pymolwiki.org/index.php/Color
    return new StructureCommand("color", getColourString(colour), atomSpec);
  }

  @Override
  protected String getResidueSpec(String residue)
  {
    // https://pymolwiki.org/index.php/Selection_Algebra
    return "resn " + residue;
  }

  @Override
  public StructureCommandI loadFile(String file)
  {
    return new StructureCommand("load", file);
  }

  /**
   * Overrides the default implementation (which generates concatenated
   * commands) to generate one per colour (because the XML-RPC interface to
   * PyMOL only accepts one command at a time)
   * 
   * @param colourMap
   * @return
   */
  @Override
  public List<StructureCommandI> colourBySequence(
          Map<Object, AtomSpecModel> colourMap)
  {
    List<StructureCommandI> commands = new ArrayList<>();
    for (Object key : colourMap.keySet())
    {
      Color colour = (Color) key;
      final AtomSpecModel colourData = colourMap.get(colour);
      commands.add(getColourCommand(colourData, colour));
    }
  
    return commands;
  }

}