VariableLengthMarkovChain.hpp

/*
 *       VariableLengthMarkovChain.hpp
 *
 *       Copyright 2011 Andre Yoshiaki Kashiwabara <akashiwabara@usp.br>
 *                      Ígor Bonádio <ibonadio@ime.usp.br>
 *                      Vitor Onuchic <vitoronuchic@gmail.com>
 *                      Alan Mitchell Durham <aland@usp.br>
 *
 *       This program 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.
 *
 *       This program 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 this program; if not, write to the Free Software
 *       Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
 *       MA 02110-1301, USA.
 */

#ifndef VLMC_MARKOV_CHAIN_HPP
#define VLMC_MARKOV_CHAIN_HPP

#include "crossplatform.hpp"

#include "ProbabilisticModel.hpp"
#include "Sequence.hpp"
#include "FactorableModel.hpp"
#include "ContextTree.hpp"


#include <boost/shared_ptr.hpp>


namespace tops{


  class DLLEXPORT VariableLengthMarkovChain : public FactorableModel {
  public:
    VariableLengthMarkovChain(){
    };

    VariableLengthMarkovChain(ContextTreePtr tree) {
      _tree = tree;
    }
    virtual ~VariableLengthMarkovChain() {};

    virtual void setTree(ContextTreePtr tree) {
      _tree = tree;
    }
    virtual ContextTreePtr getTree(){
      return _tree;
    }
    std::string print_graph () const ;
    virtual double evaluatePosition(const Sequence & s, unsigned int i) const;

    virtual double choosePosition(const Sequence & s, int i) const ;

    virtual std::string str() const ;

    virtual std::string model_name () const {
      return "VariableLengthMarkovChain";
    }

    virtual ProbabilisticModelCreatorPtr getFactory() const ;

    virtual int size() const;

    virtual void initialize(const ProbabilisticModelParameters & p) ;

    virtual ProbabilisticModelParameters parameters() const;

    virtual void removeSequenceFromModel(const Sequence & s,  int phase);
  private:
    ContextTreePtr _tree;

    void printDistribution(ContextTreePtr tree, ContextTreeNodePtr node, std::stringstream & out, AlphabetPtr alphabet) const ;


  };
  typedef boost::shared_ptr<VariableLengthMarkovChain> VariableLengthMarkovChainPtr;
}

#endif