/*
 * 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 java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.TreeMap;

/**
 * A class to model a Chimera or Jmol residue set, as
 * {@code Map<modelNumber, Map<chainId, List<residueRange>>>}. This can then be
 * traversed to generate the required display command in Chimera or Jmol syntax.
 */
public class AtomSpecModel
{
  private Map<Integer, Map<String, List<int[]>>> atomSpec;

  /**
   * Constructor
   */
  public AtomSpecModel()
  {
    atomSpec = new TreeMap<>();
  }

  public Map<Integer, Map<String, List<int[]>>> getMap()
  {
    return atomSpec;
  }

  /**
   * Adds one contiguous range to this atom spec
   * 
   * @param model
   * @param startPos
   * @param endPos
   * @param chain
   */
  public void addRange(int model, int startPos, int endPos, String chain)
  {
    /*
     * Get/initialize map of data for the colour and model
     */
    Map<String, List<int[]>> modelData = atomSpec.get(model);
    if (modelData == null)
    {
      atomSpec.put(model, modelData = new TreeMap<>());
    }

    /*
     * Get/initialize map of data for colour, model and chain
     */
    List<int[]> chainData = modelData.get(chain);
    if (chainData == null)
    {
      chainData = new ArrayList<>();
      modelData.put(chain, chainData);
    }

    /*
     * Add the start/end positions
     */
    chainData.add(new int[] { startPos, endPos });
    // TODO add intelligently, using a RangeList class
  }

  /**
   * Answers an iterable set of the structure models in this model
   * 
   * @return
   */
  public Iterable<Integer> getModels()
  {
    return atomSpec.keySet();
  }

  /**
   * Answers an iterable set of the chains in this model for the given structure
   * model, or an empty set if none
   * 
   * @param model
   * @return
   */
  public Iterable<String> getChains(Integer model)
  {
    if (atomSpec.containsKey(model))
    {
      return atomSpec.get(model).keySet();
    }
    return Collections.emptySet();
  }

  public List<int[]> getRanges(Integer model, String chain)
  {
    Map<String, List<int[]>> modelData = atomSpec.get(model);
    if (modelData != null)
    {
      List<int[]> chainData = modelData.get(chain);
      if (chainData != null)
      {
        return chainData;
      }
    }
    return Collections.EMPTY_LIST;
  }
}