ProteinFrequencySet.h

Go to the documentation of this file.

// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_FREQUENCYSET_PROTEINFREQUENCYSET_H
#define BPP_PHYL_MODEL_FREQUENCYSET_PROTEINFREQUENCYSET_H
 
#include <Bpp/Seq/Alphabet/ProteicAlphabet.h>
 
#include "FrequencySet.h"
 
namespace bpp
{
class ProteinFrequencySetInterface :
  public virtual FrequencySetInterface
{
public:
  ProteinFrequencySetInterface* clone() const override = 0;
 
  virtual std::shared_ptr<const ProteicAlphabet> getProteicAlphabet() const = 0;
};
 
class FullProteinFrequencySet :
  public virtual ProteinFrequencySetInterface,
  public FullFrequencySet
{
public:
  FullProteinFrequencySet(
      std::shared_ptr<const ProteicAlphabet> alphabet,
      bool allowNullFreqs = false,
      unsigned short method = 1,
      const std::string& name = "Full") :
    FullFrequencySet(
        std::make_shared<const CanonicalStateMap>(alphabet, false),
        allowNullFreqs,
        method,
        name)
  {}
 
  FullProteinFrequencySet(
      std::shared_ptr<const ProteicAlphabet> alphabet,
      const std::vector<double>& initFreqs,
      bool allowNullFreqs = false,
      unsigned short method = 1,
      const std::string& name = "Full") :
    FullFrequencySet(
        std::make_shared<const CanonicalStateMap>(alphabet, false),
        initFreqs,
        allowNullFreqs,
        method,
        name)
  {}
 
  FullProteinFrequencySet* clone() const override { return new FullProteinFrequencySet(*this); }
 
public:
  std::shared_ptr<const ProteicAlphabet> getProteicAlphabet() const override
  {
    return std::dynamic_pointer_cast<const ProteicAlphabet>(getAlphabet());
  }
};
 
class FixedProteinFrequencySet :
  public virtual ProteinFrequencySetInterface,
  public FixedFrequencySet
{
public:
  FixedProteinFrequencySet(
      std::shared_ptr<const ProteicAlphabet> alphabet,
      const std::vector<double>& initFreqs,
      const std::string& name = "Fixed") :
    FixedFrequencySet(
        std::make_shared<const CanonicalStateMap>(alphabet, false),
        initFreqs,
        name)
  {}
 
  FixedProteinFrequencySet(
      std::shared_ptr<const ProteicAlphabet> alphabet,
      const std::string& name = "Fixed") :
    FixedFrequencySet(
        std::make_shared<const CanonicalStateMap>(alphabet, false),
        name)
  {}
 
  FixedProteinFrequencySet* clone() const override { return new FixedProteinFrequencySet(*this); }
 
  std::shared_ptr<const ProteicAlphabet> getProteicAlphabet() const override
  {
    return std::dynamic_pointer_cast<const ProteicAlphabet>(getAlphabet());
  }
};
 
class UserProteinFrequencySet :
  public virtual ProteinFrequencySetInterface,
  public UserFrequencySet
{
public:
  UserProteinFrequencySet(
      std::shared_ptr<const ProteicAlphabet> alphabet,
      const std::string& path,
      size_t nCol = 1) :
    UserFrequencySet(
        std::make_shared<const CanonicalStateMap>(alphabet, false),
        path,
        nCol)
  {}
 
  UserProteinFrequencySet* clone() const override { return new UserProteinFrequencySet(*this); }
 
  std::shared_ptr<const ProteicAlphabet> getProteicAlphabet() const override
  {
    return std::dynamic_pointer_cast<const ProteicAlphabet>(getAlphabet());
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_FREQUENCYSET_PROTEINFREQUENCYSET_H