NucleotideFrequencySet.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_FREQUENCYSET_NUCLEOTIDEFREQUENCYSET_H
#define BPP_PHYL_MODEL_FREQUENCYSET_NUCLEOTIDEFREQUENCYSET_H
 
#include <Bpp/Seq/Alphabet/NucleicAlphabet.h>
 
#include "FrequencySet.h"
 
namespace bpp
{
class NucleotideFrequencySetInterface :
  public virtual FrequencySetInterface
{
public:
  NucleotideFrequencySetInterface* clone() const override = 0;
 
  virtual std::shared_ptr<const NucleicAlphabet> getNucleicAlphabet() const = 0;
};
 
  class GCFrequencySet :
  public virtual NucleotideFrequencySetInterface,
  public AbstractFrequencySet
{
public:
  GCFrequencySet(std::shared_ptr<const NucleicAlphabet> alphabet) :
    AbstractFrequencySet(std::make_shared<const CanonicalStateMap>(alphabet, false), "GC.", "GC")
  {
    addParameter_(new Parameter("GC.theta", 0.5, Parameter::PROP_CONSTRAINT_IN));
    getFreq_(0) = getFreq_(1) = getFreq_(2) = getFreq_(3) = 0.25;
  }
 
  GCFrequencySet(std::shared_ptr<const NucleicAlphabet> alphabet, double theta) :
    AbstractFrequencySet(std::make_shared<const CanonicalStateMap>(alphabet, false), "GC.", "GC")
  {
    addParameter_(new Parameter("GC.theta", theta, Parameter::PROP_CONSTRAINT_IN));
    getFreq_(0) = getFreq_(3) = (1. - theta) / 2.;
    getFreq_(1) = getFreq_(2) = theta / 2.;
  }
 
  GCFrequencySet* clone() const override
  {
    return new GCFrequencySet(*this);
  }
 
  GCFrequencySet(const GCFrequencySet& gcf) :
    AbstractFrequencySet(gcf)
  {}
 
public:
  std::shared_ptr<const NucleicAlphabet> getNucleicAlphabet() const override
  {
    return std::dynamic_pointer_cast<const NucleicAlphabet>(getAlphabet());
  }
 
  void setFrequencies(const std::vector<double>& frequencies) override;
 
protected:
  void fireParameterChanged(const ParameterList& parameters) override;
};
 
class FullNucleotideFrequencySet :
  public virtual NucleotideFrequencySetInterface,
  public AbstractFrequencySet
{
public:
  FullNucleotideFrequencySet(
      std::shared_ptr<const NucleicAlphabet> alphabet,
      bool allowNullFreqs = false,
      const std::string& name = "Full");
 
  FullNucleotideFrequencySet(
      std::shared_ptr<const NucleicAlphabet> alphabet,
      double theta, double theta1, double theta2,
      bool allowNullFreqs = false,
      const std::string& name = "Full");
 
  FullNucleotideFrequencySet* clone() const override { return new FullNucleotideFrequencySet(*this); }
 
public:
  std::shared_ptr<const NucleicAlphabet> getNucleicAlphabet() const override
  {
    return std::dynamic_pointer_cast<const NucleicAlphabet>(getAlphabet());
  }
 
  void setFrequencies(const std::vector<double>& frequencies) override;
 
protected:
  void fireParameterChanged(const ParameterList& parameters) override;
};
 
 
class FixedNucleotideFrequencySet :
  public virtual NucleotideFrequencySetInterface,
  public FixedFrequencySet
{
public:
  FixedNucleotideFrequencySet(
      std::shared_ptr<const NucleicAlphabet> alphabet,
      const std::vector<double>& initFreqs,
      const std::string& name = "Fixed") :
    FixedFrequencySet(std::make_shared<const CanonicalStateMap>(alphabet, false), initFreqs, name) {}
 
  FixedNucleotideFrequencySet(
      std::shared_ptr<const NucleicAlphabet> alphabet,
      const std::string& name = "Fixed") :
    FixedFrequencySet(std::make_shared<const CanonicalStateMap>(alphabet, false), name) {}
 
  FixedNucleotideFrequencySet* clone() const override { return new FixedNucleotideFrequencySet(*this); }
 
  std::shared_ptr<const NucleicAlphabet> getNucleicAlphabet() const override
  {
    return std::dynamic_pointer_cast<const NucleicAlphabet>(getAlphabet());
  }
};
 
class UserNucleotideFrequencySet :
  public virtual NucleotideFrequencySetInterface,
  public UserFrequencySet
{
public:
  UserNucleotideFrequencySet(
      std::shared_ptr<const NucleicAlphabet> alphabet,
      const std::string& path,
      size_t nCol = 1) :
    UserFrequencySet(std::make_shared<const CanonicalStateMap>(alphabet, false), path, nCol) {}
 
  UserNucleotideFrequencySet* clone() const override { return new UserNucleotideFrequencySet(*this); }
 
  std::shared_ptr<const NucleicAlphabet> getNucleicAlphabet() const override
  {
    return std::dynamic_pointer_cast<const NucleicAlphabet>(getAlphabet());
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_FREQUENCYSET_NUCLEOTIDEFREQUENCYSET_H