UserProteinSubstitutionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_PROTEIN_USERPROTEINSUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_PROTEIN_USERPROTEINSUBSTITUTIONMODEL_H
 
 
#include "../AbstractSubstitutionModel.h"
#include "../FrequencySet/ProteinFrequencySet.h"
#include "ProteinSubstitutionModel.h"
 
// From SeqLib:
#include <Bpp/Seq/Alphabet/ProteicAlphabet.h>
 
// From the STL:
#include <string>
 
namespace bpp
{
class UserProteinSubstitutionModel :
  public AbstractReversibleProteinSubstitutionModel
{
private:
  std::string path_;
  std::unique_ptr<ProteinFrequencySetInterface> freqSet_;
 
public:
  UserProteinSubstitutionModel(
      std::shared_ptr<const ProteicAlphabet> alpha,
      const std::string& path,
      const std::string& prefix);
 
  UserProteinSubstitutionModel(
      std::shared_ptr<const ProteicAlphabet> alpha,
      const std::string& path,
      std::unique_ptr<ProteinFrequencySetInterface> freqSet,
      const std::string& prefix,
      bool initFreqs = false
      );
 
  UserProteinSubstitutionModel(const UserProteinSubstitutionModel& model) :
    AbstractParameterAliasable(model),
    AbstractReversibleProteinSubstitutionModel(model),
    path_(model.path_),
    freqSet_(model.freqSet_->clone())
  {}
 
  UserProteinSubstitutionModel& operator=(const UserProteinSubstitutionModel& model)
  {
    AbstractParameterAliasable::operator=(model);
    AbstractReversibleProteinSubstitutionModel::operator=(model);
    path_ = model.path_;
    freqSet_.reset(model.freqSet_->clone());
    return *this;
  }
 
  virtual ~UserProteinSubstitutionModel() {}
 
  UserProteinSubstitutionModel* clone() const override { return new UserProteinSubstitutionModel(*this); }
 
public:
  std::string getName() const override;
 
  const std::string& getPath() const { return path_; }
 
  void fireParameterChanged(const ParameterList& parameters) override
  {
    freqSet_->matchParametersValues(parameters);
    freq_ = freqSet_->getFrequencies();
    AbstractReversibleSubstitutionModel::fireParameterChanged(parameters);
  }
 
  void setNamespace(const std::string& prefix) override
  {
    AbstractParameterAliasable::setNamespace(prefix);
    freqSet_->setNamespace(prefix + freqSet_->getName() + ".");
  }
 
  void setFrequencySet(const ProteinFrequencySetInterface& freqSet)
  {
    freqSet_.reset(freqSet.clone());
    resetParameters_();
    addParameters_(freqSet_->getParameters());
  }
 
  const FrequencySetInterface& frequencySet() const override
  {
    if (freqSet_)
      return *freqSet_;
    throw NullPointerException("UserProteinSubstitutionModel::frequencySet(). No associated FrequencySet.");
  }
 
  void setFreqFromData(const SequenceDataInterface& data, double pseudoCount = 0) override;
 
protected:
  void readFromFile();
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_PROTEIN_USERPROTEINSUBSTITUTIONMODEL_H