PhyloBranchMapping.h

Go to the documentation of this file.

// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MAPPING_PHYLOBRANCHMAPPING_H
#define BPP_PHYL_MAPPING_PHYLOBRANCHMAPPING_H
 
#include <Bpp/Clonable.h>
#include <Bpp/Exceptions.h>
#include <Bpp/Numeric/Number.h>
 
#include "../Tree/PhyloBranch.h"
 
namespace bpp
{
/*
 * @brief A branch with countings.
 *
 * WARNING : this class does not know anything about site
 * compression, if any. If there are site patterns, they are
 * available in ProbabilisticSubstitutionMapping class.
 *
 */
 
class PhyloBranchMapping :
  public PhyloBranch
{
protected:
  /*
   * @brief counts are stored by site / type
   *
   */
 
  VVdouble counts_;
 
public:
  PhyloBranchMapping() :
    PhyloBranch(),
    counts_()
  {}
 
  PhyloBranchMapping(double length) :
    PhyloBranch(length),
    counts_()
  {}
 
  PhyloBranchMapping(const PhyloBranch& branch) :
    PhyloBranch(branch),
    counts_()
  {}
 
  PhyloBranchMapping(const PhyloBranchMapping& branch) :
    PhyloBranch(branch),
    counts_(branch.counts_)
  {}
 
  PhyloBranchMapping& operator=(const PhyloBranchMapping& branch)
  {
    PhyloBranch::operator=(branch);
    counts_ = branch.counts_;
    return *this;
  }
 
  PhyloBranchMapping* clone() const { return new PhyloBranchMapping(*this); }
 
  ~PhyloBranchMapping()
  {}
 
  void setNumberOfSites(size_t nbSites)
  {
    VectorTools::resize2(counts_, nbSites, (counts_.size() != 0 ? counts_[0].size() : 0));
  }
 
  void setNumberOfTypes(size_t nbTypes)
  {
    VectorTools::resize2(counts_, counts_.size(), nbTypes);
  }
 
  void setNumberOfSitesAndTypes(size_t nbSites, size_t nbTypes)
  {
    VectorTools::resize2(counts_, nbSites, nbTypes);
  }
 
 
  size_t getNumberOfSites() const
  {
    return counts_.size();
  }
 
  size_t getNumberOfTypes() const
  {
    return counts_.size() ? counts_[0].size() : 0;
  }
 
  Vdouble& getSiteCount(size_t site)
  {
    return counts_[site];
  }
 
  const Vdouble& getSiteCount(size_t site) const
  {
    return counts_[site];
  }
 
  double getSiteTypeCount(size_t site, size_t type) const
  {
    if (site >= getNumberOfSites())
      throw BadSizeException("PhyloBranchMapping::getSiteTypeCount : bad site number", site, getNumberOfSites());
    if (type >= getNumberOfTypes())
      throw BadSizeException("PhyloBranchMapping::getSiteTypeCount : bad site number", type, getNumberOfTypes());
    return counts_[site][type];
  }
 
  void setSiteTypeCount(size_t site, size_t type, double value)
  {
    if (site >= getNumberOfSites())
      throw BadSizeException("PhyloBranchMapping::setSiteTypeCount : bad site number", site, getNumberOfSites());
    if (type >= getNumberOfTypes())
      throw BadSizeException("PhyloBranchMapping::setSiteTypeCount : bad type number", type, getNumberOfTypes());
    counts_[site][type] = value;
  }
 
 
  double operator()(size_t site, size_t type) const
  {
    return counts_[site][type];
  }
 
  double& operator()(size_t site, size_t type)
  {
    return counts_[site][type];
  }
 
  const VVdouble& getCounts() const
  {
    return counts_;
  }
 
  VVdouble& getCounts()
  {
    return counts_;
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_MAPPING_PHYLOBRANCHMAPPING_H