PhyloSubstitutionMapping.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MAPPING_PHYLOMAPPINGS_PHYLOSUBSTITUTIONMAPPING_H
#define BPP_PHYL_MAPPING_PHYLOMAPPINGS_PHYLOSUBSTITUTIONMAPPING_H
 
 
// From bpp-seq:
#include <Bpp/Numeric/ParameterAliasable.h>
#include <Bpp/Numeric/ParametrizableCollection.h>
#include "../SubstitutionRegister.h"
#include "../../Model/SubstitutionModel.h"
#include "../SubstitutionMappingTools.h"
 
#include <Bpp/Seq/AlphabetIndex/AlphabetIndex2.h>
 
namespace bpp
{
class PhyloSubstitutionMapping :
  public Clonable
{
public:
  PhyloSubstitutionMapping() {}
  virtual ~PhyloSubstitutionMapping() {}
 
  PhyloSubstitutionMapping* clone() const = 0;
 
public:
  virtual std::shared_ptr<const TransitionModelInterface> getModel(unsigned int branchId, size_t classIndex) const = 0;
 
  virtual bool matchParametersValues(const ParameterList& nullParams) = 0;
 
  virtual const ParameterList& getParameters() const = 0;
 
  virtual void computeNormalizations(const ParameterList& nullParams,
      short unresolvedOption = SubstitutionMappingTools::UNRESOLVED_ZERO,
      bool verbose = true) = 0;
 
  virtual bool normalizationsPerformed() const = 0;
 
  virtual bool countsPerformed() const = 0;
 
  virtual void computeCounts(short unresolvedOption = SubstitutionMappingTools::UNRESOLVED_ZERO,
      double threshold = -1, bool verbose = true) = 0;
 
  virtual ProbabilisticSubstitutionMapping& counts() = 0;
 
  virtual const ProbabilisticSubstitutionMapping& counts() const = 0;
 
  virtual ProbabilisticSubstitutionMapping& normalizations() = 0;
 
  virtual const ProbabilisticSubstitutionMapping& normalizations() const = 0;
 
  virtual void setDistances(const AlphabetIndex2& ndist) = 0;
};
} // end of namespace bpp.
#endif // BPP_PHYL_MAPPING_PHYLOMAPPINGS_PHYLOSUBSTITUTIONMAPPING_H