HmmProcessAlphabet.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LIKELIHOOD_HMMPROCESSALPHABET_H
#define BPP_PHYL_LIKELIHOOD_HMMPROCESSALPHABET_H
 
 
// From Numeric
#include <Bpp/Numeric/Hmm/HmmStateAlphabet.h>
 
#include "SubstitutionProcessCollection.h"
 
 
namespace bpp
{
class HmmProcessAlphabet :
  public virtual HmmStateAlphabet,
  public AbstractParametrizable
{
private:
  std::shared_ptr<const SubstitutionProcessCollection> processColl_;
 
  std::vector<size_t> nProc_;
 
public:
  HmmProcessAlphabet(
      std::shared_ptr<const SubstitutionProcessCollection> pSub,
      std::vector<size_t> nProc) :
    AbstractParametrizable(""),
    processColl_(pSub),
    nProc_(nProc)
  {}
 
  HmmProcessAlphabet(const HmmProcessAlphabet& hpa) :
    AbstractParametrizable(hpa),
    processColl_(hpa.processColl_),
    nProc_(hpa.nProc_)
  {}
 
  HmmProcessAlphabet& operator=(const HmmProcessAlphabet& hpa)
  {
    AbstractParametrizable::operator=(*this);
    processColl_ = hpa.processColl_;
    nProc_ = hpa.nProc_;
 
    return *this;
  }
 
  HmmProcessAlphabet* clone() const override {return new HmmProcessAlphabet(*this);}
 
  virtual ~HmmProcessAlphabet() {}
 
  const Clonable& getState(size_t stateIndex) const override
  {
    return processColl_->substitutionProcess(nProc_[stateIndex]);
  }
 
  size_t getNumberOfStates() const override
  {
    return nProc_.size();
  }
 
  bool worksWith(const HmmStateAlphabet& stateAlphabet) const override
  {
    return &stateAlphabet == this;
  }
};
}
#endif // BPP_PHYL_LIKELIHOOD_HMMPROCESSALPHABET_H