ProbabilisticSubstitutionMapping.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef _LEGACY_PROBABILISTIC_SUBSTITUTION_MAPPING_H_
#define _LEGACY_PROBABILISTIC_SUBSTITUTION_MAPPING_H_
 
#include "SubstitutionMapping.h"
#include "../../Mapping/SubstitutionCount.h" // We use the latest version of the class here
#include "../../Tree/TreeExceptions.h"
 
#include <Bpp/Text/TextTools.h>
 
// From the STL:
#include <vector>
 
namespace bpp
{
class LegacyProbabilisticSubstitutionMapping :
  public LegacyAbstractSubstitutionMapping
{
private:
  std::shared_ptr<const SubstitutionCountInterface> substitutionCount_;
 
  std::vector<std::vector<std::vector<double>>> mapping_;
 
public:
  LegacyProbabilisticSubstitutionMapping(const Tree& tree, std::shared_ptr<const SubstitutionCountInterface> sc, size_t numberOfSites) :
    LegacyAbstractSubstitutionMapping(tree),
    substitutionCount_(sc),
    mapping_(0)
  {
    setNumberOfSites(numberOfSites);
  }
 
  LegacyProbabilisticSubstitutionMapping(const Tree& tree) :
    LegacyAbstractSubstitutionMapping(tree),
    substitutionCount_(nullptr),
    mapping_(0)
  {}
 
 
  LegacyProbabilisticSubstitutionMapping* clone() const override
  {
    return new LegacyProbabilisticSubstitutionMapping(*this);
  }
 
  LegacyProbabilisticSubstitutionMapping(const LegacyProbabilisticSubstitutionMapping& psm) = default;
 
  LegacyProbabilisticSubstitutionMapping& operator=(const LegacyProbabilisticSubstitutionMapping& psm) = default;
 
  virtual ~LegacyProbabilisticSubstitutionMapping() {}
 
public:
  size_t getNumberOfSubstitutionTypes() const override
  {
    if (!substitutionCount_) return 1;
    return substitutionCount_->getNumberOfSubstitutionTypes();
  }
 
  double getNumberOfSubstitutions(int nodeId, size_t siteIndex, size_t type) const
  {
    return mapping_[siteIndex][getNodeIndex(nodeId)][type];
  }
 
  virtual std::vector<double> getNumberOfSubstitutions(int nodeId, size_t siteIndex) const
  {
    return mapping_[siteIndex][getNodeIndex(nodeId)];
  }
 
  virtual void setTree(const Tree& tree);
 
  virtual void setNumberOfSites(size_t numberOfSites) override;
 
  virtual double& operator()(size_t nodeIndex, size_t siteIndex, size_t type) override
  {
    return mapping_[siteIndex][nodeIndex][type];
  }
 
  virtual const double& operator()(size_t nodeIndex, size_t siteIndex, size_t type) const override
  {
    return mapping_[siteIndex][nodeIndex][type];
  }
 
  std::vector< std::vector<double>>& operator[](size_t siteIndex)
  {
    return mapping_[siteIndex];
  }
 
  const std::vector< std::vector<double>>& operator[](size_t siteIndex) const
  {
    return mapping_[siteIndex];
  }
};
} // end of namespace bpp.
 
#endif // _LEGACY_PROBABILISTIC_SUBSTITUTION_MAPPING_H_