AbstractSubstitutionModel.h

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//
// File: AbstractSubstitutionModel.h
// Created by: Julien Dutheil
// Created on: Tue May 27 10:31:49 2003
//

/*
   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
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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 _ABSTRACTSUBSTITUTIONMODEL_H_
#define _ABSTRACTSUBSTITUTIONMODEL_H_

#include "SubstitutionModel.h"

#include <Bpp/Numeric/AbstractParameterAliasable.h>
#include <Bpp/Numeric/VectorTools.h>

namespace bpp
{
class AbstractSubstitutionModel :
  public virtual SubstitutionModel,
  public virtual AbstractParameterAliasable
{
protected:
  const Alphabet* alphabet_;

  size_t size_;

  double rate_;

  std::vector<int> chars_;

  RowMatrix<double> generator_;

  Vdouble freq_;

  RowMatrix<double> exchangeability_;

  mutable RowMatrix<double> pijt_;
  mutable RowMatrix<double> dpijt_;
  mutable RowMatrix<double> d2pijt_;

  bool eigenDecompose_;

  Vdouble eigenValues_;

  Vdouble iEigenValues_;

  bool isDiagonalizable_;

  RowMatrix<double> rightEigenVectors_;

  bool isNonSingular_;

  RowMatrix<double> leftEigenVectors_;

  std::vector< RowMatrix<double> > vPowGen_;

  mutable RowMatrix<double> tmpMat_;
  
public:
  AbstractSubstitutionModel(const Alphabet* alpha, const std::string& prefix);

  AbstractSubstitutionModel(const AbstractSubstitutionModel& model) :
    AbstractParameterAliasable(model),
    alphabet_(model.alphabet_),
    size_(model.size_),
    rate_(model.rate_),
    chars_(model.chars_),
    generator_(model.generator_),
    freq_(model.freq_),
    exchangeability_(model.exchangeability_),
    pijt_(model.pijt_),
    dpijt_(model.dpijt_),
    d2pijt_(model.d2pijt_),
    eigenDecompose_(model.eigenDecompose_),
    eigenValues_(model.eigenValues_),
    iEigenValues_(model.iEigenValues_),
    isDiagonalizable_(model.isDiagonalizable_),
    rightEigenVectors_(model.rightEigenVectors_),
    isNonSingular_(model.isNonSingular_),
    leftEigenVectors_(model.leftEigenVectors_),
    vPowGen_(model.vPowGen_),
    tmpMat_(model.tmpMat_)
  {}

  AbstractSubstitutionModel& operator=(const AbstractSubstitutionModel& model)
  {
    AbstractParameterAliasable::operator=(model);
    alphabet_          = model.alphabet_;
    size_              = model.size_;
    rate_              = model.rate_;
    chars_             = model.chars_;
    generator_         = model.generator_;
    freq_              = model.freq_;
    exchangeability_   = model.exchangeability_;
    pijt_              = model.pijt_;
    dpijt_             = model.dpijt_;
    d2pijt_            = model.d2pijt_;
    eigenDecompose_    = model.eigenDecompose_;
    eigenValues_       = model.eigenValues_;
    iEigenValues_      = model.iEigenValues_;
    isDiagonalizable_  = model.isDiagonalizable_;
    rightEigenVectors_ = model.rightEigenVectors_;
    isNonSingular_     = model.isNonSingular_;
    leftEigenVectors_  = model.leftEigenVectors_;
    vPowGen_           = model.vPowGen_;
    tmpMat_            = model.tmpMat_;
    return *this;
  }
  
  virtual ~AbstractSubstitutionModel() {}

#ifndef NO_VIRTUAL_COV
  virtual AbstractSubstitutionModel* clone() const = 0;
#endif

public:
  const Alphabet* getAlphabet() const { return alphabet_; }

  const std::vector<int>& getAlphabetChars() const { return chars_; }

  int getAlphabetChar(size_t i) const { return chars_[i]; }

  std::vector<size_t> getModelStates(int i) const { return VectorTools::whichAll(chars_, i); }

  virtual const Vdouble& getFrequencies() const { return freq_; }

  const Matrix<double>& getGenerator() const { return generator_; }

  const Matrix<double>& getExchangeabilityMatrix() const { return exchangeability_; }

  double Sij(size_t i, size_t j) const { return exchangeability_(i, j); }

  virtual const Matrix<double>& getPij_t(double t) const;
  virtual const Matrix<double>& getdPij_dt(double t) const;
  virtual const Matrix<double>& getd2Pij_dt2(double t) const;

  const Vdouble& getEigenValues() const { return eigenValues_; }

  const Vdouble& getIEigenValues() const { return iEigenValues_; }

  bool isDiagonalizable() const { return isDiagonalizable_; }
  
  bool isNonSingular() const { return isNonSingular_; }

  const Matrix<double>& getRowLeftEigenVectors() const { return leftEigenVectors_; }

  const Matrix<double>& getColumnRightEigenVectors() const { return rightEigenVectors_; }

  virtual double freq(size_t i) const { return freq_[i]; }

  virtual double Qij(size_t i, size_t j) const { return generator_(i, j); }

  virtual double Pij_t    (size_t i, size_t j, double t) const { return getPij_t(t) (i, j); }
  virtual double dPij_dt  (size_t i, size_t j, double t) const { return getdPij_dt(t) (i, j); }
  virtual double d2Pij_dt2(size_t i, size_t j, double t) const { return getd2Pij_dt2(t) (i, j); }

  double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException);

  void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0);

  virtual void setFreq(std::map<int, double>&);

  void enableEigenDecomposition(bool yn) { eigenDecompose_ = yn; }

  bool enableEigenDecomposition() { return eigenDecompose_; }

  virtual void fireParameterChanged(const ParameterList& parameters)
  {
    AbstractParameterAliasable::fireParameterChanged(parameters);
    if ((parameters.size()!=1) || (parameters[0].getName()!=getNamespace()+"rate"))
      updateMatrices();
  }

  void addRateParameter();

protected:
  virtual void updateMatrices();

public:
  double getScale() const;

  void setScale(double scale);

  virtual double getRate() const;

  virtual void setRate(double rate);


  friend class AbstractBiblioSubstitutionModel;

};


class AbstractReversibleSubstitutionModel :
  public virtual AbstractSubstitutionModel,
  public virtual ReversibleSubstitutionModel
{
public:
  AbstractReversibleSubstitutionModel(const Alphabet* alpha, const std::string& prefix) :
    AbstractParameterAliasable(prefix),
    AbstractSubstitutionModel(alpha, prefix)
  {
    isDiagonalizable_ = true;
    isNonSingular_    = true;
  }

  virtual ~AbstractReversibleSubstitutionModel() {}

#ifndef NO_VIRTUAL_COV
  virtual AbstractReversibleSubstitutionModel* clone() const = 0;
#endif

protected:

  virtual void updateMatrices();
};

} //end of namespace bpp.

#endif  //_ABSTRACTSUBSTITUTIONMODEL_H_