SubstitutionModel.h

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//
// File: SubstitutionModel.h
// Created by: Julien Dutheil
// Created on: Mon May 26 14:52:34 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
   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 _SUBSTITUTIONMODEL_H_
#define _SUBSTITUTIONMODEL_H_

#include "FrequenciesSet/FrequenciesSet.h"
#include "StateMap.h"

// From bpp-core:
#include <Bpp/Exceptions.h>
#include <Bpp/Numeric/Parameter.h>
#include <Bpp/Numeric/ParameterList.h>
#include <Bpp/Numeric/ParameterAliasable.h>
#include <Bpp/Numeric/VectorTools.h>
#include <Bpp/Numeric/Matrix/Matrix.h>

// From bpp-seq:
#include <Bpp/Seq/Alphabet/Alphabet.h>
#include <Bpp/Seq/Container/SequenceContainer.h>

// From the STL:
#include <cstdlib>
#include <map>
#include <string>

namespace bpp
{
class SubstitutionModel;

class SubstitutionModelException :
  public Exception
{
protected:
  const SubstitutionModel* model_;

public:
  SubstitutionModelException(const std::string& text, const SubstitutionModel* sm = 0);

  SubstitutionModelException(const SubstitutionModelException& sme) :
    Exception(sme), model_(sme.model_) {}

  SubstitutionModelException& operator=(const SubstitutionModelException& sme)
  {
    Exception::operator=(sme);
    model_ = sme.model_;
    return *this;
  }

  ~SubstitutionModelException() throw ();

public:
  virtual const SubstitutionModel* getSubstitutionModel() const { return model_; }
};

class SubstitutionModel :
  public virtual ParameterAliasable
{
public:
  SubstitutionModel() {}
  virtual ~SubstitutionModel() {}

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

public:
  virtual std::string getName() const = 0;

  virtual const std::vector<int>& getAlphabetStates() const = 0;

  virtual const StateMap& getStateMap() const = 0;

  virtual std::vector<size_t> getModelStates(int code) const = 0;

  virtual std::vector<size_t> getModelStates(const std::string& code) const = 0;

  virtual int getAlphabetStateAsInt(size_t index) const = 0;
  
  virtual std::string getAlphabetStateAsChar(size_t index) const = 0;

  virtual double freq(size_t i) const = 0;

  virtual double Qij(size_t i, size_t j) const = 0;

  virtual double Pij_t(size_t i, size_t j, double t) const = 0;

  virtual double dPij_dt(size_t i, size_t j, double t) const = 0;

  virtual double d2Pij_dt2(size_t i, size_t j, double t) const = 0;

  virtual const Vdouble& getFrequencies() const = 0;

  virtual const Matrix<double>& getGenerator() const = 0;

  virtual const Matrix<double>& getExchangeabilityMatrix() const = 0;

  virtual double Sij(size_t i, size_t j) const = 0;
  virtual const Matrix<double>& getPij_t(double t) const = 0;

  virtual const Matrix<double>& getdPij_dt(double t) const = 0;

  virtual const Matrix<double>& getd2Pij_dt2(double t) const = 0;

  virtual void enableEigenDecomposition(bool yn) = 0;

  virtual bool enableEigenDecomposition() = 0;

  virtual const Vdouble& getEigenValues() const = 0;

  virtual const Vdouble& getIEigenValues() const = 0;

  virtual bool isDiagonalizable() const = 0;
  
  virtual bool isNonSingular() const = 0;

  virtual const Matrix<double>& getRowLeftEigenVectors() const = 0;

  virtual const Matrix<double>& getColumnRightEigenVectors() const = 0;

  virtual const Alphabet* getAlphabet() const = 0;

  virtual size_t getNumberOfStates() const = 0;

  virtual double getInitValue(size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) = 0;

  virtual double getScale() const = 0;

  virtual void setScale(double scale) = 0;

  virtual double getRate() const = 0;

  virtual void setRate(double rate) = 0;

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

  virtual void setFreq(std::map<int, double>& frequencies) {}

  virtual const FrequenciesSet* getFrequenciesSet() const {return NULL;}
};


class ReversibleSubstitutionModel :
  public virtual SubstitutionModel
{
public:
  ReversibleSubstitutionModel() {}
  virtual ~ReversibleSubstitutionModel() {}

#ifndef NO_VIRTUAL_COV
  ReversibleSubstitutionModel* clone() const = 0;
#endif
};

} //end of namespace bpp.

#endif  //_SUBSTITUTIONMODEL_H_