LowMemoryRescaledHmmLikelihood.h

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//
// File: LowMemoryRescaledHmmLikelihood.h
// Created by: Julien Dutheil
// Created on: Wed Dec 16 10:47 2009
//

/*
   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
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   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 _LOWMEMORYRESCALEDHMMLIKELIHOOD_H_
#define _LOWMEMORYRESCALEDHMMLIKELIHOOD_H_

#include "HmmLikelihood.h"
#include "../AbstractParametrizable.h"
#include "../Matrix/Matrix.h"

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

namespace bpp
{
class LowMemoryRescaledHmmLikelihood :
  public AbstractHmmLikelihood,
  public AbstractParametrizable
{
private:
  std::auto_ptr<HmmStateAlphabet> hiddenAlphabet_;
  std::auto_ptr<HmmTransitionMatrix> transitionMatrix_;
  std::auto_ptr<HmmEmissionProbabilities> emissionProbabilities_;

  std::vector<double> likelihood1_;
  std::vector<double> likelihood2_;
  double logLik_;
  size_t maxSize_;

  std::vector<size_t> breakPoints_;

  size_t nbStates_, nbSites_;

public:
  LowMemoryRescaledHmmLikelihood(
    HmmStateAlphabet* hiddenAlphabet,
    HmmTransitionMatrix* transitionMatrix,
    HmmEmissionProbabilities* emissionProbabilities,
    const std::string& prefix,
    size_t maxSize = 1000000) throw (Exception);

  LowMemoryRescaledHmmLikelihood(const LowMemoryRescaledHmmLikelihood& lik) :
    AbstractHmmLikelihood(lik),
    AbstractParametrizable(lik),
    hiddenAlphabet_(dynamic_cast<HmmStateAlphabet*>(lik.hiddenAlphabet_->clone())),
    transitionMatrix_(dynamic_cast<HmmTransitionMatrix*>(lik.transitionMatrix_->clone())),
    emissionProbabilities_(dynamic_cast<HmmEmissionProbabilities*>(lik.emissionProbabilities_->clone())),
    likelihood1_(lik.likelihood1_),
    likelihood2_(lik.likelihood2_),
    logLik_(lik.logLik_),
    maxSize_(lik.maxSize_),
    breakPoints_(lik.breakPoints_),
    nbStates_(lik.nbStates_),
    nbSites_(lik.nbSites_)
  {
    // Now adjust pointers:
    transitionMatrix_->setHmmStateAlphabet(hiddenAlphabet_.get());
    emissionProbabilities_->setHmmStateAlphabet(hiddenAlphabet_.get());
  }

  LowMemoryRescaledHmmLikelihood& operator=(const LowMemoryRescaledHmmLikelihood& lik)
  {
    AbstractHmmLikelihood::operator=(lik);
    AbstractParametrizable::operator=(lik);
    hiddenAlphabet_        = std::auto_ptr<HmmStateAlphabet>(dynamic_cast<HmmStateAlphabet*>(lik.hiddenAlphabet_->clone()));
    transitionMatrix_      = std::auto_ptr<HmmTransitionMatrix>(dynamic_cast<HmmTransitionMatrix*>(lik.transitionMatrix_->clone()));
    emissionProbabilities_ = std::auto_ptr<HmmEmissionProbabilities>(dynamic_cast<HmmEmissionProbabilities*>(lik.emissionProbabilities_->clone()));
    likelihood1_           = lik.likelihood1_;
    likelihood2_           = lik.likelihood2_;
    logLik_                = lik.logLik_;
    maxSize_               = lik.maxSize_;
    breakPoints_           = lik.breakPoints_;
    nbStates_              = lik.nbStates_;
    nbSites_               = lik.nbSites_;

    // Now adjust pointers:
    transitionMatrix_->setHmmStateAlphabet(hiddenAlphabet_.get());
    emissionProbabilities_->setHmmStateAlphabet(hiddenAlphabet_.get());
    return *this;
  }

  virtual ~LowMemoryRescaledHmmLikelihood() {}

#ifndef NO_VIRTUAL_COV
  LowMemoryRescaledHmmLikelihood*
#else
  Clonable*
#endif
  clone() const { return new LowMemoryRescaledHmmLikelihood(*this); }

public:
  const HmmStateAlphabet& getHmmStateAlphabet() const { return *hiddenAlphabet_; }
  HmmStateAlphabet& getHmmStateAlphabet() { return *hiddenAlphabet_; }

  const HmmTransitionMatrix& getHmmTransitionMatrix() const { return *transitionMatrix_; }
  HmmTransitionMatrix& getHmmTransitionMatrix() { return *transitionMatrix_; }

  const HmmEmissionProbabilities& getHmmEmissionProbabilities() const { return *emissionProbabilities_; }
  HmmEmissionProbabilities& getHmmEmissionProbabilities() { return *emissionProbabilities_; }

  void setBreakPoints(const std::vector<size_t>& breakPoints) {
    breakPoints_ = breakPoints;
    computeForward_();
  }

  const std::vector<size_t>& getBreakPoints() const { return breakPoints_; }

  void setParameters(const ParameterList& pl) throw (Exception)
  {
    setParametersValues(pl);
  }

  double getValue() const throw (Exception) { return -logLik_; }

  double getLogLikelihood() const { return logLik_; }

  void fireParameterChanged(const ParameterList& pl);


  double getLikelihoodForASite(size_t site) const
  {
    throw (NotImplementedException("LowMemoryRescaledHmmLikelihood::getLikelihoodForASite. This class can't compute posterior probabilities, use RescaledHmmLikelihood instead."));    
  }


  Vdouble getLikelihoodForEachSite() const
  {
    throw (NotImplementedException("LowMemoryRescaledHmmLikelihood::getLikelihoodForEachSite. This class can't compute posterior probabilities, use RescaledHmmLikelihood instead."));    
  }

  Vdouble getHiddenStatesPosteriorProbabilitiesForASite(size_t site) const
  {
    throw (NotImplementedException("LowMemoryRescaledHmmLikelihood::getHiddenStatesPosteriorProbabilitiesForASite. This class can't compute posterior probabilities, use RescaledHmmLikelihood instead."));    
  }

  void getHiddenStatesPosteriorProbabilities(std::vector< std::vector<double> >& probs, bool append = false) const throw (NotImplementedException)
  {
    throw (NotImplementedException("LowMemoryRescaledHmmLikelihood::getHiddenStatesPosteriorProbabilities. This class can't compute posterior probabilities, use RescaledHmmLikelihood instead."));    
  }

protected:
  void computeForward_();

  void computeDLikelihood_() const
  {
    //    computeDForward_();
  }

  void computeD2Likelihood_() const
  {
    //    computeD2Forward_();
  }
};

}

#endif // _LOWMEMORYRESCALEDHMMLIKELIHOOD_H_