SitePatterns.h

Go to the documentation of this file.

// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_SITEPATTERNS_H
#define BPP_PHYL_SITEPATTERNS_H
 
#include <Bpp/Clonable.h>
#include <Bpp/Numeric/VectorTools.h>
 
 
// From bpp-seq:
#include <Bpp/Seq/CoreSite.h>
#include <Bpp/Seq/Container/SiteContainer.h>
 
// From the STL:
#include <map>
#include <vector>
#include <string>
 
#include <Eigen/Core>
 
namespace bpp
{
class SitePatterns :
  public virtual Clonable
{
public:
  typedef Eigen::Matrix<size_t, 1, -1> IndicesType;
 
private:
  class SortableSite
  {
public:
    std::string siteS;
    const CoreSiteInterface* siteP;
    size_t originalPosition;
 
public:
    SortableSite() : siteS(), siteP(0), originalPosition(0) {}
    SortableSite(const SortableSite& ss) : siteS(ss.siteS), siteP(ss.siteP), originalPosition(ss.originalPosition) {}
    SortableSite& operator=(const SortableSite& ss)
    {
      siteS = ss.siteS;
      siteP = ss.siteP;
      originalPosition = ss.originalPosition;
      return *this;
    }
 
    bool operator<(const SortableSite& ss) const { return siteS < ss.siteS; }
 
    virtual ~SortableSite() {}
  };
 
private:
  std::vector<std::string> names_;
  std::vector<std::shared_ptr<const CoreSiteInterface>> sites_;
  std::vector<unsigned int> weights_;
  IndicesType indices_;
  std::shared_ptr<const Alphabet> alpha_;
 
public:
  SitePatterns(
      const AlignmentDataInterface& sequences,
      std::vector<std::string> names = {});
 
  SitePatterns* clone() const { return new SitePatterns(*this); }
 
private:
  void init_(
      const AlignmentDataInterface& sequences,
      std::vector<std::string> names = {});
 
public:
  const std::vector<unsigned int>& getWeights() const { return weights_; }
  const IndicesType& getIndices() const { return indices_; }
 
  std::unique_ptr<AlignmentDataInterface> getSites() const;
};
} // end of namespace bpp.
#endif // BPP_PHYL_SITEPATTERNS_H