AbstractSubstitutionProcess.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LIKELIHOOD_ABSTRACTSUBSTITUTIONPROCESS_H
#define BPP_PHYL_LIKELIHOOD_ABSTRACTSUBSTITUTIONPROCESS_H
 
 
#include "SubstitutionProcess.h"
 
// From the STL:
#include <memory>
 
// From bpp-core:
#include <Bpp/Numeric/AbstractParameterAliasable.h>
 
namespace bpp
{
class AbstractSubstitutionProcess :
  public virtual SubstitutionProcessInterface,
  public virtual AbstractParameterAliasable
{
public:
  AbstractSubstitutionProcess() :
    AbstractParameterAliasable("")
  {}
 
  size_t getNumberOfClasses() const
  {
    auto dist = getRateDistribution();
    return dist ? dist->getNumberOfCategories() : 1;
  }
 
  size_t getNumberOfStates() const
  {
    return stateMap().getNumberOfModelStates();
  }
 
  std::shared_ptr<const Alphabet> getAlphabet() const
  {
    return stateMap().getAlphabet();
  }
 
  bool isCompatibleWith(const AlignmentDataInterface& data) const
  {
    return data.getAlphabet()->getAlphabetType() == getAlphabet()->getAlphabetType();
  }
 
  ParameterList getNonDerivableParameters() const;
};
} // end namespace bpp
#endif // BPP_PHYL_LIKELIHOOD_ABSTRACTSUBSTITUTIONPROCESS_H