Simplex.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1

#ifndef BPP_NUMERIC_PROB_SIMPLEX_H
#define BPP_NUMERIC_PROB_SIMPLEX_H


// From the STL:
#include <vector>

#include "../AbstractParameterAliasable.h"

namespace bpp
{
class Simplex :
  public AbstractParameterAliasable
{
private:
  size_t dim_;

  unsigned short method_;

  std::vector<double> vProb_;

  std::vector<double> valpha_;

public:
  Simplex(size_t dim, unsigned short method = 0, bool allowNull = false, const std::string& name = "Simplex.");

  Simplex(const std::vector<double>& probas, unsigned short method = 0, bool allowNull = false, const std::string& name = "Simplex.");

  virtual ~Simplex() {}

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

public:
  void fireParameterChanged(const ParameterList& parameters);

  size_t dimension() const { return dim_; }

  void setFrequencies(const std::vector<double>&);

  const std::vector<double>& getFrequencies() const { return vProb_;}

  std::vector<double>& getFrequencies() { return vProb_;}

  double prob(size_t i) const { return vProb_[i]; }

  unsigned short getMethod() const { return method_; }
};

class OrderedSimplex :
  public Simplex
{
private:
  std::vector<double> vValues_;

public:
  OrderedSimplex(size_t dim, unsigned short method = 0, bool allowNull = false, const std::string& name = "Simplex.") :
    Simplex(dim, method, allowNull, name),
    vValues_(dim)
  {
    const auto& probs = Simplex::getFrequencies();

    double x = 0;
    for (auto i = dim; i > 0; i--)
    {
      x += probs[i - 1] / (int)i;
      vValues_[i - 1] = x;
    }
  }


  OrderedSimplex(const std::vector<double>& probas, unsigned short method = 0, bool allowNull = false, const std::string& name = "Simplex.");

  void fireParameterChanged(const ParameterList& parameters);

  void setFrequencies(const std::vector<double>&);

  const std::vector<double>& getFrequencies() const { return vValues_;}
};
} // end of namespace bpp.

#endif // BPP_NUMERIC_PROB_SIMPLEX_H