NullPrefixSumArray.hpp

/*
 *       NullPrefixSumArray.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 NULL_PREFIX_SUM_ARRAY_HPP
#define NULL_PREFIX_SUM_ARRAY_HPP

#include "crossplatform.hpp"

#include <boost/shared_ptr.hpp>
#include "Sequence.hpp"
#include "ProbabilisticModel.hpp"
namespace tops {

  class DLLEXPORT NullPrefixSumArray : public PrefixSumArray
  {
  private:
    ProbabilisticModel *_model;
    Sequence _s;
  public:
    NullPrefixSumArray(ProbabilisticModel *model): _model(model){}
    virtual ~NullPrefixSumArray(){};

    virtual void initialize(const Sequence & s) {
      initialize(s, 0);
    }

    virtual void initialize(const Sequence & s, int phase) {
      _s = s;
    }

    virtual double compute(int begin, int end ) const {
      return  _model->evaluate(_s, begin,end);
    }

    virtual double compute (int begin, int end, int start_phase) const {
      return compute(begin, end);
    }
  };

typedef boost::shared_ptr <NullPrefixSumArray> NullPrefixSumArrayPtr;
}

#endif