StateMap.h

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//
// 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
{

  class StateMap:
    public virtual Clonable
  {
    public:
      virtual ~StateMap() {}
      virtual StateMap* clone() const = 0;

    public:
      virtual const Alphabet* getAlphabet() const = 0;

      virtual size_t getNumberOfModelStates() const = 0;

      virtual const std::vector<int>& getAlphabetStates() const = 0;

      virtual std::string getAlphabetStateAsChar(size_t index) const = 0;

      virtual int getAlphabetStateAsInt(size_t index) const = 0;

      virtual std::vector<size_t> getModelStates(const std::string& code) const = 0;

      virtual std::vector<size_t> getModelStates(int code) const = 0;
      
  };

  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));
      }

  };

  class CanonicalStateMap:
    public AbstractStateMap
  {
    public:
      CanonicalStateMap(const Alphabet* alphabet, bool includeGaps);

      CanonicalStateMap(const StateMap& sm, bool includeGaps);

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

  };


  
  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_