AbstractWrappedModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_ABSTRACTWRAPPEDMODEL_H
#define BPP_PHYL_MODEL_ABSTRACTWRAPPEDMODEL_H
 
#include <Bpp/Seq/Container/SequenceContainerTools.h>
#include <Bpp/Seq/Container/SequenceData.h>
 
#include "WrappedModel.h"
#include "AbstractSubstitutionModel.h"
 
namespace bpp
{
class AbstractWrappedModel :
  public virtual AbstractParameterAliasable,
  public virtual WrappedModelInterface
{
public:
  AbstractWrappedModel(const std::string& prefix) :
    AbstractParameterAliasable(prefix)
  {}
 
  virtual ~AbstractWrappedModel() {}
 
public:
  const std::vector<int>& getAlphabetStates() const override { return model().getAlphabetStates(); }
 
  const StateMapInterface& stateMap() const override { return model().stateMap(); }
 
  std::shared_ptr<const StateMapInterface> getStateMap() const override { return model().getStateMap(); }
 
  int getAlphabetStateAsInt(size_t i) const override { return model().getAlphabetStateAsInt(i); }
 
  std::string getAlphabetStateAsChar(size_t i) const override { return model().getAlphabetStateAsChar(i); }
 
  std::vector<size_t> getModelStates(int code) const override { return model().getModelStates(code); }
 
  std::vector<size_t> getModelStates(const std::string& code) const override { return model().getModelStates(code); }
 
 
  const Alphabet& alphabet() const override { return model().alphabet(); }
 
  std::shared_ptr<const Alphabet> getAlphabet() const override { return model().getAlphabet(); }
 
  size_t getNumberOfStates() const override { return model().getNumberOfStates(); }
 
  const FrequencySetInterface& frequencySet() const override
  {
    return model().frequencySet();
  }
 
  virtual std::string getName() const override
  {
    return model().getName();
  }
};
 
class AbstractWrappedTransitionModel :
  public virtual AbstractWrappedModel,
  public virtual AbstractLkTransitionModel,
  public virtual WrappedTransitionModelInterface
{
public:
  AbstractWrappedTransitionModel(const std::string& prefix) :
    AbstractWrappedModel(prefix)
  {}
 
protected:
  BranchModelInterface& model_()
  {
    return transitionModel_();
  }
 
  virtual TransitionModelInterface& transitionModel_() = 0;
 
public:
  const FrequencySetInterface& frequencySet() const override
  {
    return transitionModel().frequencySet();
  }
 
  const BranchModelInterface& model() const override
  {
    return transitionModel();
  }
};
 
 
class AbstractTotallyWrappedTransitionModel :
  public virtual AbstractWrappedTransitionModel
{
public:
  AbstractTotallyWrappedTransitionModel(const std::string& prefix) :
    AbstractWrappedTransitionModel(prefix) {}
 
  virtual ~AbstractTotallyWrappedTransitionModel() {}
 
public:
  double freq(size_t i) const override { return transitionModel().freq(i); }
 
  double Pij_t    (size_t i, size_t j, double t) const override { return transitionModel().Pij_t(i, j, t); }
  double dPij_dt  (size_t i, size_t j, double t) const override { return transitionModel().dPij_dt (i, j, t); }
  double d2Pij_dt2(size_t i, size_t j, double t) const override { return transitionModel().d2Pij_dt2(i, j, t); }
 
  const Vdouble& getFrequencies() const override { return transitionModel().getFrequencies(); }
 
  const Matrix<double>& getPij_t(double t) const override { return transitionModel().getPij_t(t); }
 
  const Matrix<double>& getdPij_dt(double t) const override { return transitionModel().getdPij_dt(t); }
 
  const Matrix<double>& getd2Pij_dt2(double t) const override { return transitionModel().getd2Pij_dt2(t); }
 
  double getInitValue(size_t i, int state) const override
  {
    return transitionModel().getInitValue(i, state);
  }
 
  double getRate() const override
  {
    return transitionModel().getRate();
  }
 
  void setRate(double rate) override
  {
    return transitionModel_().setRate(rate);
  }
 
  void setFreqFromData(const SequenceDataInterface& data, double pseudoCount = 0) override
  {
    std::map<int, double> freqs;
    SequenceContainerTools::getFrequencies(data, freqs, pseudoCount);
    // Re-compute generator and eigen values:
    transitionModel_().setFreq(freqs);
  }
 
  void setFreq(std::map<int, double>& frequencies) override
  {
    transitionModel_().setFreq(frequencies);
  }
 
  bool computeFrequencies() const override
  {
    return transitionModel().computeFrequencies();
  }
 
  void computeFrequencies(bool yn) override
  {
    transitionModel_().computeFrequencies(yn);
  }
 
protected:
  Vdouble& getFrequencies_() override
  {
    return transitionModel_().getFrequencies_();
  }
};
 
 
class AbstractWrappedSubstitutionModel :
  public virtual AbstractWrappedTransitionModel,
  public virtual WrappedSubstitutionModelInterface
{
public:
  AbstractWrappedSubstitutionModel(const std::string& prefix) :
    AbstractWrappedTransitionModel(prefix)
  {}
 
  virtual ~AbstractWrappedSubstitutionModel() {}
 
  const TransitionModelInterface& transitionModel() const
  {
    return substitutionModel();
  }
 
protected:
  TransitionModelInterface& transitionModel_()
  {
    return substitutionModel_();
  }
 
  virtual SubstitutionModelInterface& substitutionModel_() = 0;
};
 
class AbstractTotallyWrappedSubstitutionModel :
  public virtual AbstractTotallyWrappedTransitionModel,
  public virtual AbstractWrappedSubstitutionModel
{
public:
  AbstractTotallyWrappedSubstitutionModel(const std::string& prefix) :
    AbstractTotallyWrappedTransitionModel(prefix),
    AbstractWrappedSubstitutionModel(prefix)
  {}
 
  virtual ~AbstractTotallyWrappedSubstitutionModel() {}
 
  double Qij(size_t i, size_t j) const { return substitutionModel().Qij(i, j); }
 
  const Matrix<double>& generator() const { return substitutionModel().generator(); }
 
  const Matrix<double>& exchangeabilityMatrix() const { return substitutionModel().exchangeabilityMatrix(); }
 
  double Sij(size_t i, size_t j) const { return substitutionModel().Sij(i, j); }
 
  void enableEigenDecomposition(bool yn) { substitutionModel_().enableEigenDecomposition(yn); }
 
  bool enableEigenDecomposition() { return substitutionModel_().enableEigenDecomposition(); }
 
  bool isDiagonalizable() const { return substitutionModel().isDiagonalizable(); }
 
  bool isNonSingular() const { return substitutionModel().isNonSingular(); }
 
  const Vdouble& getEigenValues() const { return substitutionModel().getEigenValues(); }
 
  const Vdouble& getIEigenValues() const { return substitutionModel().getIEigenValues(); }
 
  const Matrix<double>& getRowLeftEigenVectors() const { return substitutionModel().getRowLeftEigenVectors(); }
 
  const Matrix<double>& getColumnRightEigenVectors() const { return substitutionModel().getColumnRightEigenVectors(); }
 
 
  bool isScalable() const
  {
    return substitutionModel().isScalable();
  }
 
  void setScalable(bool scalable)
  {
    substitutionModel_().setScalable(scalable);
  }
 
  void normalize()
  {
    substitutionModel_().normalize();
  }
 
  void setDiagonal()
  {
    substitutionModel_().setDiagonal();
  }
 
  double getScale() const
  {
    return substitutionModel().getScale();
  }
 
  void setScale(double scale)
  {
    substitutionModel_().setScale(scale);
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_ABSTRACTWRAPPEDMODEL_H