MarkovModulatedSubstitutionModel.h

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//
// File: MarkovModulatedSubstitutionModel.h
// Created by: Julien Dutheil
// Created on: Sat Aug 05 08:21 2006
//

/*
  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 _MARKOVMODULATEDSUBSTITUTIONMODEL_H_
#define _MARKOVMODULATEDSUBSTITUTIONMODEL_H_

#include "SubstitutionModel.h"

#include <Bpp/Numeric/AbstractParameterAliasable.h>
#include <Bpp/Numeric/Matrix/MatrixTools.h>

namespace bpp
{

  class MarkovModulatedSubstitutionModel:
    public virtual ReversibleSubstitutionModel,
    public AbstractParameterAliasable
  {

  protected:
    ReversibleSubstitutionModel* model_;
    MarkovModulatedStateMap stateMap_;
    size_t nbStates_; //Number of states in model
    size_t nbRates_; //Number of rate classes

    RowMatrix<double> rates_;                //All rates values
    RowMatrix<double> ratesExchangeability_; //All rates transitions
    Vdouble           ratesFreq_;            //All rates equilibrium frequencies
    RowMatrix<double> ratesGenerator_;       //All rates transitions
    
    RowMatrix<double> generator_;

    RowMatrix<double> exchangeability_;

    RowMatrix<double> leftEigenVectors_;

    RowMatrix<double> rightEigenVectors_;

    Vdouble eigenValues_;

    Vdouble iEigenValues_;

    bool eigenDecompose_;

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

    Vdouble freq_;

    bool normalizeRateChanges_;

    std::string nestedPrefix_;

  public:
    MarkovModulatedSubstitutionModel(ReversibleSubstitutionModel* model, unsigned int nbRates, bool normalizeRateChanges, const std::string& prefix) :
      AbstractParameterAliasable(prefix),
      model_(model), stateMap_(model->getStateMap(), nbRates), nbStates_(model->getNumberOfStates()),
      nbRates_(nbRates), rates_(nbRates, nbRates), ratesExchangeability_(nbRates, nbRates),
      ratesFreq_(nbRates), ratesGenerator_(nbRates, nbRates), generator_(), exchangeability_(),
      leftEigenVectors_(), rightEigenVectors_(), eigenValues_(), iEigenValues_(), eigenDecompose_(true), 
      pijt_(), dpijt_(), d2pijt_(), freq_(),
      normalizeRateChanges_(normalizeRateChanges),
      nestedPrefix_("model_" + model->getNamespace())
    {
      model_->setNamespace(prefix + nestedPrefix_);
      addParameters_(model_->getIndependentParameters());
    }
    
    MarkovModulatedSubstitutionModel(const MarkovModulatedSubstitutionModel& model);
    MarkovModulatedSubstitutionModel& operator=(const MarkovModulatedSubstitutionModel& model);

    virtual ~MarkovModulatedSubstitutionModel() { delete model_; }

#ifndef NO_VIRTUAL_COV
    MarkovModulatedSubstitutionModel*
#else
    Clonable*
#endif
    clone() const = 0;

  public:
    
    const Alphabet* getAlphabet() const { return model_->getAlphabet(); }

    size_t getNumberOfStates() const { return nbStates_ * nbRates_; }

    const StateMap& getStateMap() const { return stateMap_; }

    const std::vector<int>& getAlphabetStates() const { return stateMap_.getAlphabetStates(); }

    std::string getAlphabetStateAsChar(size_t index) const { return stateMap_.getAlphabetStateAsChar(index); }

    int getAlphabetStateAsInt(size_t index) const { return stateMap_.getAlphabetStateAsInt(index); }

    std::vector<size_t> getModelStates(int code) const { return stateMap_.getModelStates(code); }
  
    std::vector<size_t> getModelStates(const std::string& code) const { return stateMap_.getModelStates(code); }

    const Vdouble& getFrequencies() const { return freq_; }
    
    const Matrix<double>& getExchangeabilityMatrix() const { return exchangeability_; }
    
    const Matrix<double>& getGenerator() const { return generator_; }
    
    const Matrix<double>& getPij_t(double t) const;
    const Matrix<double>& getdPij_dt(double t) const;
    const Matrix<double>& getd2Pij_dt2(double t) const;
    
    const Vdouble& getEigenValues() const { return eigenValues_; }
    const Vdouble& getIEigenValues() const { return iEigenValues_; }

    bool isDiagonalizable() const { return true; }
    bool isNonSingular() const { return true; }

    const Matrix<double>& getRowLeftEigenVectors() const { return leftEigenVectors_; }
    const Matrix<double>& getColumnRightEigenVectors() const { return rightEigenVectors_; }
    
    double freq(size_t i) const { return freq_[i]; }
    double Sij(size_t i, size_t j) const { return exchangeability_(i, j); }
    double Qij(size_t i, size_t j) const { return generator_(i, j); }
    
    double Pij_t    (size_t i, size_t j, double t) const { return getPij_t(t)(i, j); }
    double dPij_dt  (size_t i, size_t j, double t) const { return getdPij_dt(t)(i, j); }
    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)
    {
      model_->setFreqFromData(data, pseudoCount);
      updateMatrices();
    }


    const ReversibleSubstitutionModel* getNestedModel() const { return model_; }

    size_t getRate(size_t i) const
    {
      return i / nbStates_; 
    }

    double getRate() const { return model_->getRate(); }

    void setRate(double rate) { model_->setRate(rate); }

    double getScale() const
    {
      std::vector<double> v;
      MatrixTools::diag(generator_, v);
      return -VectorTools::scalar<double, double>(v, freq_);
    }

    void setScale(double scale) {
      model_->setScale(scale);
      updateMatrices();
    } 

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

    bool enableEigenDecomposition() { return eigenDecompose_; }
  
    virtual void fireParameterChanged(const ParameterList& parameters)
    {
      AbstractParameterAliasable::fireParameterChanged(parameters);
      model_->matchParametersValues(parameters);
      updateRatesModel();
      updateMatrices();
    }
   
    void setNamespace(const std::string& prefix);

  protected:
    
    virtual void updateMatrices();

    virtual void updateRatesModel() = 0;

  };

} //end of namespace bpp.

#endif //_MARKOVMODULATEDSUBSTITUTIONMODEL_H_