/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
 * 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.ext.rbvi.chimera;

import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.util.Format;

import java.awt.Color;
import java.util.ArrayList;
import java.util.Hashtable;

/**
 * Routines for generating Chimera commands for Jalview/Chimera binding
 * 
 * @author JimP
 * 
 */
public class ChimeraCommands
{

  /**
   * utility to construct the commands to colour chains by the given alignment
   * for passing to Chimera
   * 
   * @returns Object[] { Object[] { <model being coloured>,
   * 
   */
  public static StructureMappingcommandSet[] getColourBySequenceCommand(
          StructureSelectionManager ssm, String[] files,
          SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
          AlignmentI alignment)
  {

    ArrayList<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
    Hashtable<String,StringBuffer> colranges=new Hashtable<String,StringBuffer>();
    for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
    {
      float cols[] = new float[4];
      StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
      StringBuffer command = new StringBuffer();
      StructureMappingcommandSet smc;
      ArrayList<String> str = new ArrayList<String>();

      if (mapping == null || mapping.length < 1)
        continue;

      int startPos = -1, lastPos = -1, startModel = -1, lastModel = -1;
      String startChain = "", lastChain = "";
      Color lastCol = null;
      for (int s = 0; s < sequence[pdbfnum].length; s++)
      {
        for (int sp, m = 0; m < mapping.length; m++)
        {
          if (mapping[m].getSequence() == sequence[pdbfnum][s]
                  && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
          {
            SequenceI asp = alignment.getSequenceAt(sp);
            for (int r = 0; r < asp.getLength(); r++)
            {
              // no mapping to gaps in sequence
              if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
              {
                continue;
              }
              int pos = mapping[m].getPDBResNum(asp.findPosition(r));

              if (pos < 1 || pos == lastPos)
                continue;

              Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);

              if (fr != null)
                col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
              if (lastCol != col || lastPos + 1 != pos
                      || pdbfnum != lastModel
                      || !mapping[m].getChain().equals(lastChain))
              {
                if (lastCol != null)
                {
                  addColourRange(colranges, lastCol,startModel,startPos,lastPos,lastChain); 
                }
                lastCol = null;
                startPos = pos;
                startModel = pdbfnum;
                startChain = mapping[m].getChain();
              }
              lastCol = col;
              lastPos = pos;
              lastModel = pdbfnum;
              lastChain = mapping[m].getChain();
            }
            // final colour range
            if (lastCol != null)
            {
              addColourRange(colranges, lastCol,startModel,startPos,lastPos,lastChain); 
            }
            break;
          }
        }
      }
      // Finally, add the command set ready to be returned.
      StringBuffer coms=new StringBuffer();
      for (String cr:colranges.keySet())
      {
        coms.append("color #"+cr+" "+colranges.get(cr)+";");
      }
      cset.add(new StructureMappingcommandSet(ChimeraCommands.class,
              files[pdbfnum], new String[] { coms.toString() }));
    }
    return cset.toArray(new StructureMappingcommandSet[cset.size()]);
  }

  private static void addColourRange(Hashtable<String, StringBuffer> colranges, Color lastCol, int startModel,
          int startPos, int lastPos, String lastChain)
  {
    
    String colstring = ((lastCol.getRed()< 16) ? "0":"")+Integer.toHexString(lastCol.getRed())
            + ((lastCol.getGreen()< 16) ? "0":"")+Integer.toHexString(lastCol.getGreen())
            + ((lastCol.getBlue()< 16) ? "0":"")+Integer.toHexString(lastCol.getBlue());
    StringBuffer currange = colranges.get(colstring);
    if (currange==null)
    {
      colranges.put(colstring,currange = new StringBuffer());
    }
    if (currange.length()>0)
    {
      currange.append("|");
    }
    currange.append("#" + startModel + ":" + ((startPos==lastPos) ? startPos : startPos + "-"
            + lastPos) + "." + lastChain);
  }

}