HmmLikelihood.h

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

#ifndef BPP_NUMERIC_HMM_HMMLIKELIHOOD_H
#define BPP_NUMERIC_HMM_HMMLIKELIHOOD_H


// From NumCalc:
#include "../Function/Functions.h"
#include "../VectorTools.h"

#include "HmmStateAlphabet.h"
#include "HmmTransitionMatrix.h"
#include "HmmEmissionProbabilities.h"

namespace bpp
{
class HmmLikelihood :
  public virtual SecondOrderDerivable
{
public:
  virtual HmmLikelihood* clone() const = 0;

  virtual const HmmStateAlphabet& hmmStateAlphabet() const = 0;
  virtual HmmStateAlphabet& hmmStateAlphabet() = 0;

  virtual std::shared_ptr<const HmmStateAlphabet> getHmmStateAlphabet() const = 0;
  virtual std::shared_ptr<HmmStateAlphabet> getHmmStateAlphabet() = 0;

  virtual const HmmTransitionMatrix& hmmTransitionMatrix() const = 0;
  virtual HmmTransitionMatrix& hmmTransitionMatrix() = 0;

  virtual std::shared_ptr<const HmmTransitionMatrix> getHmmTransitionMatrix() const = 0;
  virtual std::shared_ptr<HmmTransitionMatrix> getHmmTransitionMatrix() = 0;

  virtual const HmmEmissionProbabilities& hmmEmissionProbabilities() const = 0;
  virtual HmmEmissionProbabilities& hmmEmissionProbabilities() = 0;

  virtual std::shared_ptr<const HmmEmissionProbabilities> getHmmEmissionProbabilities() const = 0;
  virtual std::shared_ptr<HmmEmissionProbabilities> getHmmEmissionProbabilities() = 0;

  virtual void getHiddenStatesPosteriorProbabilities(std::vector< std::vector<double>>& probs, bool append) const = 0;

  virtual Vdouble getHiddenStatesPosteriorProbabilitiesForASite(size_t site) const = 0;

  virtual double getLogLikelihood() const = 0;

  virtual double getDLogLikelihood() const = 0;

  virtual double getD2LogLikelihood() const = 0;

  virtual double getLikelihoodForASite(size_t site) const = 0;

  virtual double getDLogLikelihoodForASite(size_t site) const = 0;

  virtual double getD2LogLikelihoodForASite(size_t site) const = 0;

  virtual Vdouble getLikelihoodForEachSite() const = 0;

  virtual const std::vector<size_t>& getBreakPoints() const = 0;

  virtual void setBreakPoints(const std::vector<size_t>& breakPoints) = 0;

protected:
  virtual void computeDLikelihood_() const = 0;

  virtual void computeD2Likelihood_() const = 0;
};


class AbstractHmmLikelihood :
  public virtual HmmLikelihood
{
protected:
  mutable double dLogLik_;
  mutable std::string dVariable_;

  mutable double d2LogLik_;
  mutable std::string d2Variable_;

public:
  AbstractHmmLikelihood();

  AbstractHmmLikelihood(const AbstractHmmLikelihood& adhlik);

  AbstractHmmLikelihood& operator=(const AbstractHmmLikelihood& adhlik);

  void enableFirstOrderDerivatives(bool yn) {}

  bool enableFirstOrderDerivatives() const { return true;}

  double getFirstOrderDerivative(const std::string& variable) const;

  double getDLogLikelihood() const
  {
    return dLogLik_;
  }

  void enableSecondOrderDerivatives(bool yn) {}

  bool enableSecondOrderDerivatives() const {return true;}

  double getSecondOrderDerivative(const std::string& variable) const;

  double getD2LogLikelihood() const
  {
    return d2LogLik_;
  }

  double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const
  {
    throw (NotImplementedException("AbstractHmmLikelihood::getSecondOrderDerivative is not defined for 2 variables."));
  }

};
} // end of namespace bpp.
#endif // BPP_NUMERIC_HMM_HMMLIKELIHOOD_H