SubstitutionRegister.h

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//
// File: SubstitutionRegister.h
// Created by: Julien Dutheil
// Created on: Mon Dec 6 16:32 2010
//

/*
   Copyright or © or Copr. Bio++ Development Team, (November 16, 2004, 2005, 2006)

   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 _SUBSTITUTIONREGISTER_H_
#define _SUBSTITUTIONREGISTER_H_

#include "../Model/SubstitutionModel.h"
#include "../Model/Nucleotide/NucleotideSubstitutionModel.h"
#include "../Model/Codon/CodonSubstitutionModel.h"

// From bpp-core:
#include <Bpp/Clonable.h>
#include <Bpp/Numeric/Matrix/Matrix.h>
#include <Bpp/Text/StringTokenizer.h>

// From bpp-seq:
#include <Bpp/Seq/Alphabet/NucleicAlphabet.h>
#include <Bpp/Seq/Alphabet/CodonAlphabet.h>
#include <Bpp/Seq/GeneticCode/GeneticCode.h>

// From the STL:
#include <vector>
#include <string>
#include <algorithm>

namespace bpp
{
class SubstitutionRegister :
  public virtual Clonable
{
public:
  SubstitutionRegister() {}
  virtual ~SubstitutionRegister() {}

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

public:
  virtual const Alphabet* getAlphabet() const = 0;

  virtual const SubstitutionModel* getSubstitutionModel() const = 0;

  virtual size_t getNumberOfSubstitutionTypes() const = 0;

  virtual size_t getType(size_t fromState, size_t toState) const = 0;

  virtual std::string getTypeName(size_t type) const = 0;
};

class AbstractSubstitutionRegister :
  public virtual SubstitutionRegister
{
protected:
  const SubstitutionModel* model_;

public:
  AbstractSubstitutionRegister(const SubstitutionModel* model) :
    model_(model)
  {}

  AbstractSubstitutionRegister(const AbstractSubstitutionRegister& asr) :
    model_(asr.model_)
  {}

  AbstractSubstitutionRegister& operator=(const AbstractSubstitutionRegister& asr)
  {
    model_ = asr.model_;
    return *this;
  }

  virtual ~AbstractSubstitutionRegister() {}

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

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

class CategorySubstitutionRegister :
  public AbstractSubstitutionRegister
{
protected:
  bool within_;
  size_t nbCategories_;
  mutable std::map<int, size_t> categories_;
  std::vector<std::string> categoryNames_;
  std::vector< std::vector<size_t> > index_;
  std::vector< std::vector<size_t> > revIndex_;

public:
  CategorySubstitutionRegister(const SubstitutionModel* model, bool within = false) :
    AbstractSubstitutionRegister(model),
    within_(within),
    nbCategories_(0),
    categories_(),
    categoryNames_(),
    index_(),
    revIndex_()
  {}

protected:
  template<class T>
  void setCategories(const std::map<int, T>& categories)
  {
    // First index categories:
    nbCategories_ = 0;
    std::map<T, size_t> cats;
    for (typename std::map<int, T>::const_iterator it = categories.begin(); it != categories.end(); ++it)
    {
      if (cats.find(it->second) == cats.end())
      {
        ++nbCategories_;
        cats[it->second] = nbCategories_;
      }
    }

    // Now creates categories:
    categories_.clear();
    categoryNames_.resize(nbCategories_);
    std::vector<int> types = model_->getAlphabetStates();
    for (size_t i = 0; i < types.size(); ++i)
    {
      typename std::map<int, T>::const_iterator it = categories.find(types[i]);
      if (it != categories.end())
      {
        categories_[types[i]] = cats[it->second];
        categoryNames_[cats[it->second] - 1] += model_->getAlphabet()->intToChar(types[i]);
      }
      else
      {
        categories_[types[i]] = 0;
      }
    }

    size_t count = 1;
    index_.resize(nbCategories_);
    for (size_t i = 0; i < index_.size(); ++i)
    {
      index_[i].resize(nbCategories_);
      for (size_t j = 0; j < index_.size(); ++j)
      {
        if (j != i)
        {
          index_[i][j] = count++;
          std::vector<size_t> pos(2);
          pos[0] = i;
          pos[1] = j;
          revIndex_.push_back(pos);
        }
      }
    }
    if (within_)
    {
      for (size_t i = 0; i < index_.size(); ++i)
      {
        index_[i][i] = count++;
        std::vector<size_t> pos(2);
        pos[0] = i;
        pos[1] = i;
        revIndex_.push_back(pos);
      }
    }
  }

public:
  virtual size_t getCategory(size_t state) const
  {
    int alphabetState = model_->getAlphabetStateAsInt(state);
    return categories_[alphabetState];
  }

  virtual size_t getCategoryFrom(size_t type) const
  {
    if (type <= nbCategories_ * (nbCategories_ - 1))
    {
      return revIndex_[type - 1][0] + 1;
    }
    else
    {
      if (within_)
        return revIndex_[type - 1][0] + 1;
      else
        throw Exception("CategorySubstitutionRegister::getCategoryFrom. Bad substitution type.");
    }
  }

  virtual size_t getCategoryTo(size_t type) const
  {
    if (type <= nbCategories_ * (nbCategories_ - 1))
    {
      return revIndex_[type - 1][1] + 1;
    }
    else
    {
      if (within_)
        return revIndex_[type - 1][1] + 1;
      else
        throw Exception("CategorySubstitutionRegister::getCategoryTo. Bad substitution type.");
    }
  }

  virtual std::string getCategoryName(size_t category) const
  {
    return categoryNames_[category - 1];
  }

  virtual bool allowWithin() const { return within_; }

  size_t getNumberOfCategories() const { return nbCategories_; }

  size_t getNumberOfSubstitutionTypes() const { return nbCategories_ * (nbCategories_ - 1) + (within_ ? nbCategories_ : 0); }

  virtual size_t getType(size_t fromState, size_t toState) const
  {
    size_t fromCat = categories_[model_->getAlphabetStateAsInt(fromState)];
    size_t toCat   = categories_[model_->getAlphabetStateAsInt(toState)];
    if (fromCat > 0 && toCat > 0)
      return index_[fromCat - 1][toCat - 1];
    else
      return 0;
  }

  std::string getTypeName(size_t type) const
  {
    return getCategoryName(getCategoryFrom(type)) + "->" +  getCategoryName(getCategoryTo(type));
  }
};


class TotalSubstitutionRegister :
  public AbstractSubstitutionRegister
{
public:
  TotalSubstitutionRegister(const SubstitutionModel* model) :
    AbstractSubstitutionRegister(model)
  {}

  TotalSubstitutionRegister* clone() const { return new TotalSubstitutionRegister(*this); }

public:
  size_t getNumberOfSubstitutionTypes() const { return 1; }

  size_t getType(size_t fromState, size_t toState) const
  {
    return fromState == toState ? 0 : 1;
  }

  std::string getTypeName(size_t type) const
  {
    if (type == 0)
    {
      return "no substitution";
    }
    else if (type == 1)
    {
      return "substitution";
    }
    else
    {
      throw Exception("TotalSubstitutionRegister::getTypeName. Bad substitution type.");
    }
  }
};

class CompleteSubstitutionRegister :
  public AbstractSubstitutionRegister
{
private:
  const SubstitutionRegister* preg_;

  bool isRegComplete_;

public:
  CompleteSubstitutionRegister(const SubstitutionRegister& reg) :
    AbstractSubstitutionRegister(reg.getSubstitutionModel()),
    preg_(reg.clone()),
    isRegComplete_(true)
  {
    size_t size = reg.getAlphabet()->getSize();
    for (size_t i = 0; i < size; i++)
    {
      for (size_t j = 0; j < size; j++)
      {
        if ((i != j) && reg.getType(i, j) == 0)
        {
          isRegComplete_ = false;
          return;
        }
      }
    }
  }

  CompleteSubstitutionRegister* clone() const { return new CompleteSubstitutionRegister(*this); }

  CompleteSubstitutionRegister(const CompleteSubstitutionRegister& csr) :
    AbstractSubstitutionRegister(csr),
    preg_(csr.preg_->clone()),
    isRegComplete_(csr.isRegComplete_)
  {}

  CompleteSubstitutionRegister& operator=(const CompleteSubstitutionRegister& csr)
  {
    AbstractSubstitutionRegister::operator=(csr);
    preg_ = csr.preg_->clone();
    isRegComplete_ = csr.isRegComplete_;
    return *this;
  }

  ~CompleteSubstitutionRegister()
  {
    if (preg_)
      delete preg_;
    preg_ = 0;
  }

public:
  size_t getNumberOfSubstitutionTypes() const
  {
    return preg_->getNumberOfSubstitutionTypes() + (isRegComplete_ ? 0 : 1);
  }

  size_t getType(size_t fromState, size_t toState) const
  {
    size_t t = preg_->getType(fromState, toState);
    if (t == 0)
      return getNumberOfSubstitutionTypes();
    else
      return t;
  }

  std::string getTypeName(size_t type) const
  {
    try
    {
      return preg_->getTypeName(type);
    }
    catch (Exception& e)
    {
      if (type == getNumberOfSubstitutionTypes())
        return "Completion substitution";
      else
        throw Exception("CompleteSubstitutionRegister::getTypeName. Bad substitution type.");
    }
  }
};

class ComprehensiveSubstitutionRegister :
  public CategorySubstitutionRegister
{
public:
  ComprehensiveSubstitutionRegister(const SubstitutionModel* model, bool within = false) :
    CategorySubstitutionRegister(model, within)
  {
    std::map<int, int> categories;
    for (int i = 0; i < static_cast<int>(model->getAlphabet()->getSize()); ++i)
    {
      categories[i] = i;
    }
    setCategories<int>(categories);
  }

  ComprehensiveSubstitutionRegister* clone() const { return new ComprehensiveSubstitutionRegister(*this); }
};

class GeneralSubstitutionRegister :
  public AbstractSubstitutionRegister
{
protected:
  size_t size_;

  RowMatrix<size_t> matrix_;

  std::map<size_t, std::map<size_t, std::vector<size_t> > > types_;

public:
  GeneralSubstitutionRegister(const SubstitutionModel* model) :
    AbstractSubstitutionRegister(model),
    size_(model->getNumberOfStates()),
    matrix_(size_, size_),
    types_()
  {}

  GeneralSubstitutionRegister(const SubstitutionModel* model, const RowMatrix<size_t>& matrix) :
    AbstractSubstitutionRegister(model),
    size_(model->getNumberOfStates()),
    matrix_(matrix),
    types_()
  {
    if (matrix_.getNumberOfRows() != size_)
      throw DimensionException("GeneralSubstitutionRegister", size_, matrix_.getNumberOfRows());
    if (matrix_.getNumberOfColumns() != size_)
      throw DimensionException("GeneralSubstitutionRegister", size_, matrix_.getNumberOfColumns());
    updateTypes_();
  }

  GeneralSubstitutionRegister(const GeneralSubstitutionRegister& gsr) :
    AbstractSubstitutionRegister(gsr),
    size_(gsr.size_),
    matrix_(gsr.matrix_),
    types_(gsr.types_)
  {}

  GeneralSubstitutionRegister& operator=(const GeneralSubstitutionRegister& gsr)
  {
    AbstractSubstitutionRegister::operator=(gsr);
    size_   = gsr.size_;
    matrix_ = gsr.matrix_;
    types_  = gsr.types_;
    return *this;
  }

  GeneralSubstitutionRegister* clone() const { return new GeneralSubstitutionRegister(*this); }

  virtual ~GeneralSubstitutionRegister() {}

  size_t getType(size_t i, size_t j) const
  {
    return matrix_(i, j);
  }

  size_t getNumberOfSubstitutionTypes() const
  {
    return types_.find(0) == types_.end() ? types_.size() : types_.size() - 1;
  }

  std::string getTypeName(size_t type) const
  {
    if (types_.find(type) != types_.end())
      return TextTools::toString(type);

    throw Exception("Bad type number " + TextTools::toString(type) + " in GeneralSubstitutionRegister::getTypeName.");
  }

protected:
  void updateTypes_();
};


class SelectedSubstitutionRegister :
  public GeneralSubstitutionRegister
{
  std::map<size_t, std::string> categoryNames_;

public:
  SelectedSubstitutionRegister (const SubstitutionModel* model, std::string selectedSubstitutions) :
    GeneralSubstitutionRegister(model),
    categoryNames_()
  {
    selectedSubstitutions.erase(std::remove(selectedSubstitutions.begin(), selectedSubstitutions.end(), ' '), selectedSubstitutions.end());
    size_t typeSubs = 0;
    size_t coord1 = 0;
    size_t coord2 = 0;
    std::string codon1 = "";
    std::string codon2 = "";
    StringTokenizer subsGroup(selectedSubstitutions, "()");
    while (subsGroup.hasMoreToken())
    {
      typeSubs++;
      StringTokenizer namesSubs(subsGroup.nextToken(), ":");
      if (namesSubs.numberOfRemainingTokens() == 2)
      {
        categoryNames_[typeSubs] = namesSubs.nextToken();
      }
      else if (namesSubs.numberOfRemainingTokens() == 1)
      {
        categoryNames_[typeSubs] = TextTools::toString(typeSubs);
      }
      StringTokenizer substitutions(namesSubs.nextToken(), ",");
      while (substitutions.hasMoreToken())
      {
        StringTokenizer coordinates(substitutions.nextToken(), "->");
        codon1 = coordinates.nextToken();
        codon2 = coordinates.nextToken();
        coord1 = model_->getAlphabet()->getStateIndex(codon1);
        coord2 = model_->getAlphabet()->getStateIndex(codon2);
        this->matrix_(coord1, coord2) = typeSubs;
      }
    }
    updateTypes_();
  }

  SelectedSubstitutionRegister* clone() const { return new SelectedSubstitutionRegister(*this); }

  ~SelectedSubstitutionRegister() {}

  std::string getTypeName(size_t type) const
  {
    if (types_.find(type) != types_.end())
      return TextTools::toString(categoryNames_.find(type)->second);

    throw Exception("Bad type number " + TextTools::toString(type) + " in GeneralSubstitutionRegister::getTypeName.");
  }
};

class AAInteriorSubstitutionRegister :
  public GeneralSubstitutionRegister
{
  std::map<std::string, size_t> categoryCorrespondance_;

public:
  AAInteriorSubstitutionRegister(const CodonSubstitutionModel* model) :
    GeneralSubstitutionRegister(model),
    categoryCorrespondance_()
  {
    size_t categoryIndex = 1;
    for (size_t i = 0; i < model->getAlphabet()->getSize(); ++i)
    {
      int state1 = model->getAlphabet()->getStateAt(i).getNum();
      for (size_t j = i + 1; j < model->getAlphabet()->getSize(); ++j)
      {
        int state2 = model->getAlphabet()->getStateAt(j).getNum();
        if (!(model->getGeneticCode()->isStop(state1)) && !(model->getGeneticCode()->isStop(state2)))
        {
          if (model->getGeneticCode()->translate(state1) == model->getGeneticCode()->translate(state2))
          {
            std::string aminoAcid = model->getGeneticCode()->getTargetAlphabet()->intToChar(model->getGeneticCode()->translate(state1));
            if (categoryCorrespondance_.find(aminoAcid) == categoryCorrespondance_.end())
            {
              categoryCorrespondance_[aminoAcid] = categoryIndex;
              categoryIndex++;
            }
            matrix_(i, j) = categoryCorrespondance_[aminoAcid];
            matrix_(j, i) = categoryCorrespondance_[aminoAcid];
          }
        }
      }
    }
    updateTypes_();
  }

  AAInteriorSubstitutionRegister* clone() const { return new AAInteriorSubstitutionRegister(*this); }

  ~AAInteriorSubstitutionRegister() {}


  std::string getTypeName(size_t type) const
  {
    if (types_.find(type) != types_.end())
    {
      for (std::map<std::string, size_t>::const_iterator it = categoryCorrespondance_.begin(); it != categoryCorrespondance_.end(); it++)
      {
        if (it->second == type)
          return TextTools::toString(it->first);
      }
    }
    throw Exception("Bad type number " + TextTools::toString(type) + " in GeneralSubstitutionRegister::getTypeName.");
  }
};

class AAExteriorSubstitutionRegister :
  public GeneralSubstitutionRegister
{
  std::map<std::string, size_t> categoryCorrespondance_;

public:
  AAExteriorSubstitutionRegister (const CodonSubstitutionModel* model) :
    GeneralSubstitutionRegister(model),
    categoryCorrespondance_()
  {
    size_t categoryIndex = 1;
    for (size_t i = 0; i < model->getAlphabet()->getSize(); ++i)
    {
      int state1 = model->getAlphabet()->getStateAt(i).getNum();
      for (size_t j = i + 1; j < model->getAlphabet()->getSize(); ++j)
      {
        int state2 = model->getAlphabet()->getStateAt(j).getNum();
        if (!(model->getGeneticCode()->isStop(state1)) && !(model->getGeneticCode()->isStop(state2)))
        {
          if (model->getGeneticCode()->translate(state1) != model->getGeneticCode()->translate(state2))
          {
            std::string aminoAcid1 = model->getGeneticCode()->getTargetAlphabet()->intToChar(model->getGeneticCode()->translate(state1));
            std::string aminoAcid2 = model->getGeneticCode()->getTargetAlphabet()->intToChar(model->getGeneticCode()->translate(state2));
            bool AA1IsNotInGroup = ((categoryCorrespondance_.find(aminoAcid1 + "->" + aminoAcid2) == categoryCorrespondance_.end()));
            bool AA2IsNotInGroup = ((categoryCorrespondance_.find(aminoAcid2 + "->" + aminoAcid1) == categoryCorrespondance_.end()));
            if (AA1IsNotInGroup)
            {
              categoryCorrespondance_[aminoAcid1 + "->" + aminoAcid2] = categoryIndex;
              categoryIndex++;
            }
            this->matrix_(i, j) = categoryCorrespondance_[aminoAcid1 + "->" + aminoAcid2];
            if (AA2IsNotInGroup)
            {
              categoryCorrespondance_[aminoAcid2 + "->" + aminoAcid1] = categoryIndex;
              categoryIndex++;
            }
            this->matrix_(j, i) = categoryCorrespondance_[aminoAcid2 + "->" + aminoAcid1];
          }
        }
      }
    }
    updateTypes_();
  }

  AAExteriorSubstitutionRegister* clone() const { return new AAExteriorSubstitutionRegister(*this); }

  ~AAExteriorSubstitutionRegister() {}

  std::string getTypeName(size_t type) const
  {
    if (types_.find(type) != types_.end())
    {
      for (std::map<std::string, size_t>::const_iterator it = categoryCorrespondance_.begin(); it != categoryCorrespondance_.end(); it++)
      {
        if (it->second == type)
          return TextTools::toString(it->first);
      }
    }
    throw Exception("Bad type number " + TextTools::toString(type) + " in GeneralSubstitutionRegister::getTypeName.");
  }
};

class GCSubstitutionRegister :
  public CategorySubstitutionRegister
{
public:
  GCSubstitutionRegister(const NucleotideSubstitutionModel* model, bool within = false) :
    CategorySubstitutionRegister(model, within)
  {
    std::map<int, int> categories;
    categories[0] = 1;
    categories[1] = 2;
    categories[2] = 2;
    categories[3] = 1;
    setCategories<int>(categories);
  }

  GCSubstitutionRegister* clone() const { return new GCSubstitutionRegister(*this); }
};

class TsTvSubstitutionRegister :
  public AbstractSubstitutionRegister
{
public:
  TsTvSubstitutionRegister(const NucleotideSubstitutionModel* model) :
    AbstractSubstitutionRegister(model)
  {}

  TsTvSubstitutionRegister* clone() const { return new TsTvSubstitutionRegister(*this); }

public:
  size_t getNumberOfSubstitutionTypes() const { return 2; }

  size_t getType(size_t fromState, size_t toState) const
  {
    int x = model_->getAlphabetStateAsInt(fromState);
    int y = model_->getAlphabetStateAsInt(toState);
    if (x == y)
      return 0;                     // nothing happens
    if ((x == 0 && y == 2)
        || (x == 2 && y == 0)
        || (x == 1 && y == 3)
        || (x == 3 && y == 1))
      return 1;                     // This is a transition
    return 2; // This is a transversion
  }

  std::string getTypeName(size_t type) const
  {
    if (type == 0)
    {
      return "no substitution";
    }
    else if (type == 1)
    {
      return "transition";
    }
    else if (type == 2)
    {
      return "transversion";
    }
    else
    {
      throw Exception("TsTvSubstitutionRegister::getTypeName. Bad substitution type.");
    }
  }
};

class DnDsSubstitutionRegister :
  public AbstractSubstitutionRegister
{
private:
  const GeneticCode* code_;
  bool countMultiple_;

public:
  DnDsSubstitutionRegister(const CodonSubstitutionModel* model, bool countMultiple = false) :
    AbstractSubstitutionRegister(model),
    code_(model->getGeneticCode()),
    countMultiple_(countMultiple)
  {}

  DnDsSubstitutionRegister(const DnDsSubstitutionRegister& reg) :
    AbstractSubstitutionRegister(reg),
    code_(reg.code_),
    countMultiple_(reg.countMultiple_)
  {}

  DnDsSubstitutionRegister& operator=(const DnDsSubstitutionRegister& reg)
  {
    AbstractSubstitutionRegister::operator=(reg);
    code_ = reg.code_;
    countMultiple_ = reg.countMultiple_;
    return *this;
  }

  DnDsSubstitutionRegister* clone() const { return new DnDsSubstitutionRegister(*this); }

public:
  size_t getNumberOfSubstitutionTypes() const { return 2; }

  size_t getType(size_t fromState, size_t toState) const
  {
    int x = model_->getAlphabetStateAsInt(fromState);
    int y = model_->getAlphabetStateAsInt(toState);
    const CodonAlphabet* cAlpha = dynamic_cast<const CodonAlphabet*>(model_->getAlphabet());
    if (code_->isStop(x) || code_->isStop(y))
      return 0;
    if (x == y)
      return 0;                     // nothing happens
    if (!countMultiple_)
    {
      size_t countPos = 0;
      if (cAlpha->getFirstPosition(x) != cAlpha->getFirstPosition(y))
        countPos++;
      if (cAlpha->getSecondPosition(x) != cAlpha->getSecondPosition(y))
        countPos++;
      if (cAlpha->getThirdPosition(x) != cAlpha->getThirdPosition(y))
        countPos++;
      if (countPos > 1)
        return 0;
    }
    return code_->areSynonymous(x, y) ? 1 : 2;
  }

  std::string getTypeName (size_t type) const
  {
    if (type == 0)
    {
      return "no substitution";
    }
    else if (type == 1)
    {
      return "synonymous";
    }
    else if (type == 2)
    {
      return "non synonymous";
    }
    else
    {
      throw Exception("DnDsSubstitutionRegister::getTypeName. Bad substitution type.");
    }
  }
};

class GCSynonymousSubstitutionRegister :
  public CategorySubstitutionRegister
{
private:
  const GeneticCode* code_;

public:
  GCSynonymousSubstitutionRegister(const CodonSubstitutionModel* model, bool within = false) :
    CategorySubstitutionRegister(model, within),
    code_(model->getGeneticCode())
  {
    const CodonAlphabet* pCA = dynamic_cast<const CodonAlphabet*>(code_->getSourceAlphabet());

    std::map<int, int> categories;
    for (int i = 0; i < static_cast<int>(pCA->getSize()); i++)
    {
      int n = pCA->getThirdPosition(i);
      switch (n)
      {
      case 0:
      case 3:
        categories[i] = 1;
        break;
      case 1:
      case 2:
        categories[i] = 2;
        break;
      }
    }
    setCategories<int>(categories);
  }

  GCSynonymousSubstitutionRegister(const GCSynonymousSubstitutionRegister& reg) :
    CategorySubstitutionRegister(reg),
    code_(reg.code_)
  {}

  GCSynonymousSubstitutionRegister& operator=(const GCSynonymousSubstitutionRegister& reg)
  {
    CategorySubstitutionRegister::operator=(reg);
    code_ = reg.code_;
    return *this;
  }

  GCSynonymousSubstitutionRegister* clone() const { return new GCSynonymousSubstitutionRegister(*this); }

public:
  size_t getNumberOfSubstitutionTypes() const { return 2; }

  size_t getType(size_t fromState, size_t toState) const
  {
    int x = model_->getAlphabetStateAsInt(fromState);
    int y = model_->getAlphabetStateAsInt(toState);
    const CodonAlphabet* pCA = dynamic_cast<const CodonAlphabet*>(code_->getSourceAlphabet());
    if (code_->isStop(x) || code_->isStop( y) || !code_->areSynonymous(x, y))
      return 0;

    // only substitutions between 3rd positions

    if ((pCA->getFirstPosition(x) != pCA->getFirstPosition(y)) ||
        (pCA->getSecondPosition(x) != pCA->getSecondPosition(y)))
      return 0;

    size_t fromCat = categories_[x];
    size_t toCat   = categories_[y];

    if (fromCat > 0 && toCat > 0)
      return index_[fromCat - 1][toCat - 1];
    else
      return 0;
  }

  std::string getTypeName (size_t type) const
  {
    if (type == 0)
    {
      return "no AT<->GC substitution or non-synonymous substitution";
    }
    else if (type == 1)
    {
      return "AT->GC synonymous";
    }
    else if (type == 2)
    {
      return "GC->AT synonymous";
    }
    else
    {
      throw Exception("GCSynonymousSubstitutionRegister::getTypeName. Bad substitution type.");
    }
  }
};
} // end of namespace bpp.

#endif // _SUBSTITUTIONREGISTER_H_