MultiProcessSequenceEvolution.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LIKELIHOOD_MULTIPROCESSSEQUENCEEVOLUTION_H
#define BPP_PHYL_LIKELIHOOD_MULTIPROCESSSEQUENCEEVOLUTION_H
 
#include <Bpp/Numeric/AbstractParametrizable.h>
 
#include "SequenceEvolution.h"
#include "SubstitutionProcess.h"
#include "SubstitutionProcessCollection.h"
 
// From SeqLib:
#include <Bpp/Seq/Container/AlignmentData.h>
 
using namespace std;
 
namespace bpp
{
class MultiProcessSequenceEvolution :
  virtual public SequenceEvolution,
  public AbstractParameterAliasable
{
protected:
  std::shared_ptr<SubstitutionProcessCollection> processColl_;
 
  std::vector<size_t> nProc_;
 
public:
  MultiProcessSequenceEvolution(
      std::shared_ptr<SubstitutionProcessCollection> processColl,
      std::vector<size_t> nProc,
      const std::string& prefix = "");
 
  MultiProcessSequenceEvolution(const MultiProcessSequenceEvolution& lik) :
    AbstractParameterAliasable(lik),
    processColl_(lik.processColl_),
    nProc_(lik.nProc_)
  {}
 
  MultiProcessSequenceEvolution& operator=(const MultiProcessSequenceEvolution& lik)
  {
    AbstractParameterAliasable::operator=(lik);
 
    processColl_ = lik.processColl_;
    nProc_ = lik.nProc_;
 
    return *this;
  }
 
public:
  const SubstitutionProcessCollection& collection() const { return *processColl_; }
 
  std::shared_ptr<const SubstitutionProcessCollection> getCollection() const { return processColl_; }
 
  SubstitutionProcessCollection& collection() { return *processColl_; }
 
  std::shared_ptr<SubstitutionProcessCollection> getCollection() { return processColl_; }
 
  size_t getNumberOfSubstitutionProcess() const { return nProc_.size(); }
 
  const SubstitutionProcessInterface& substitutionProcess(size_t number) const
  {
    return processColl_->substitutionProcess(number);
  }
 
  std::shared_ptr<const SubstitutionProcessInterface> getSubstitutionProcess(size_t number) const
  {
    return processColl_->getSubstitutionProcess(number);
  }
 
  const std::vector<size_t>& getSubstitutionProcessNumbers() const
  {
    return nProc_;
  }
 
  ParameterList getSubstitutionProcessParameters(bool independent) const;
 
  ParameterList getSubstitutionModelParameters(bool independent) const;
 
  ParameterList getRateDistributionParameters(bool independent) const;
 
  ParameterList getRootFrequenciesParameters(bool independent) const;
 
  ParameterList getBranchLengthParameters(bool independent) const;
 
  virtual ParameterList getNonDerivableParameters() const;
 
  virtual void fireParameterChanged(const ParameterList& parameters);
 
  void setParameters(const ParameterList& parameters);
 
  virtual bool isCompatibleWith(const AlignmentDataInterface& data) const;
};
} // end of namespace bpp.
#endif // BPP_PHYL_LIKELIHOOD_MULTIPROCESSSEQUENCEEVOLUTION_H