//
// File: StateMap.h
// Created by: Julien Dutheil
// Created on: Wed Jun 13 15:03 2012
//

/*
   Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)

   This software is a computer program whose purpose is to provide classes
   for phylogenetic data analysis.

   This software is governed by the CeCILL  license under French law and
   abiding by the rules of distribution of free software.  You can  use,
   modify and/ or redistribute the software under the terms of the CeCILL
   license as circulated by CEA, CNRS and INRIA at the following URL
   "http://www.cecill.info".

   As a counterpart to the access to the source code and  rights to copy,
   modify and redistribute granted by the license, users are provided only
   with a limited warranty  and the software's author,  the holder of the
   economic rights,  and the successive licensors  have only  limited
   liability.

   In this respect, the user's attention is drawn to the risks associated
   with loading,  using,  modifying and/or developing or reproducing the
   software by the user in light of its specific status of free software,
   that may mean  that it is complicated to manipulate,  and  that  also
   therefore means  that it is reserved for developers  and  experienced
   professionals having in-depth computer knowledge. Users are therefore
   encouraged to load and test the software's suitability as regards their
   requirements in conditions enabling the security of their systems and/or
   data to be ensured and,  more generally, to use and operate it in the
   same conditions as regards security.

   The fact that you are presently reading this means that you have had
   knowledge of the CeCILL license and that you accept its terms.
 */

#ifndef _STATEMAP_H_
#define _STATEMAP_H_

#include <Bpp/Clonable.h>
#include <Bpp/Seq/Alphabet/Alphabet.h>
#include <Bpp/Seq/Alphabet/NucleicAlphabet.h>
#include <Bpp/Numeric/VectorTools.h>

//From the STL:
#include <vector>
#include <string>

namespace bpp
{

  /**
   * @brief Map the states of a given alphabet which have a model state.
   */
  class StateMap:
    public virtual Clonable
  {
    public:
      virtual ~StateMap() {}
      virtual StateMap* clone() const = 0;

    public:
      /**
       * @return The associated alphabet.
       */
      virtual const Alphabet* getAlphabet() const = 0;

      /**
       * @return The number of states supported by the model.
       */
      virtual size_t getNumberOfModelStates() const = 0;

      /**
       * @return A vector with the corresponding alphabet states for each model state.
       * the size of the vector is the number of model states, not the number of supported alphabet states,
       * as distinct model states can correspond to a single alphabet state.
       */
      virtual const std::vector<int>& getAlphabetStates() const = 0;

      /**
       * @param index The model state.
       * @return The corresponding alphabet state as character code.
       */
      virtual std::string getAlphabetStateAsChar(size_t index) const = 0;

      /**
       * @param index The model state.
       * @return The corresponding alphabet state as int code.
       */
      virtual int getAlphabetStateAsInt(size_t index) const = 0;

      /**
       * @param code The character code of the alphabet state to check.
       * @return The corresponding model states, is any.
       */
      virtual std::vector<size_t> getModelStates(const std::string& code) const = 0;

      /**
       * @param code The int code of the alphabet state to check.
       * @return The corresponding model states, is any.
       */
      virtual std::vector<size_t> getModelStates(int code) const = 0;
      
  };

  /**
   * @brief A convenience partial implementation of the StateMap interface.
   *
   * Model states are stored as their corresponding int codes, stored in a vector 'states_'.
   * This vector has to be initialized and filled by the derived class.
   */
  class AbstractStateMap:
    public virtual StateMap
  {
    protected:
      const Alphabet* alphabet_;
      std::vector<int> states_;

    public:
      AbstractStateMap(const Alphabet* alphabet):
        alphabet_(alphabet),
        states_()
      {}

      AbstractStateMap(const AbstractStateMap& absm):
        alphabet_(absm.alphabet_),
        states_(absm.states_)
      {}

      AbstractStateMap& operator=(const AbstractStateMap& absm)
      {
        alphabet_ = absm.alphabet_;
        states_ = absm.states_;
        return *this;
      }

    public:
      virtual const Alphabet* getAlphabet() const { return alphabet_; }
      virtual size_t getNumberOfModelStates() const { return states_.size(); }
      virtual const std::vector<int>& getAlphabetStates() const { return states_; }
      virtual int getAlphabetStateAsInt(size_t index) const { return states_[index]; }
      virtual std::string getAlphabetStateAsChar(size_t index) const { return alphabet_->intToChar(states_[index]); }
      virtual std::vector<size_t> getModelStates(int code) const {
        return VectorTools::whichAll(states_, code);
      }
      virtual std::vector<size_t> getModelStates(const std::string& code) const {
        return VectorTools::whichAll(states_, alphabet_->charToInt(code));
      }

  };

  /**
   * @brief This class implements a state map where all resolved states are modeled.
   *
   * For nucleotides, the underlying states are for instance: A (0), C (1), G (2), T/U (3).
   * Optionally, gaps can be modeled.
   */
  class CanonicalStateMap:
    public AbstractStateMap
  {
    public:
      CanonicalStateMap(const Alphabet* alphabet, bool includeGaps);

      /**
       * @brief this contructors takes an existing StateMap and adds one model states for gaps.
       * If the original StateMap alread had a state for gaps, a new one will be appended.
       */
      CanonicalStateMap(const StateMap& sm, bool includeGaps);

      virtual CanonicalStateMap* clone() const { return new CanonicalStateMap(*this); }

  };


  
  /**
   * @brief This class implements a state map for Markov modulated models.
   *
   * For nucleotides with two classes, the underlying states are for instance:
   * A (0), C (1), G (2), T/U (3), A (4), C (5), G (6), T/U (7).
   */
  class MarkovModulatedStateMap:
    public AbstractStateMap
  {
    public:
      MarkovModulatedStateMap(const StateMap& unitMap, unsigned int nbClasses);
      virtual MarkovModulatedStateMap* clone() const { return new MarkovModulatedStateMap(*this); }

  };

}// end of namespace bpp

#endif //_STATEMAP_H_

