ProbabilisticSubstitutionMapping.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MAPPING_PROBABILISTICSUBSTITUTIONMAPPING_H
#define BPP_PHYL_MAPPING_PROBABILISTICSUBSTITUTIONMAPPING_H
 
#include <Bpp/Text/TextTools.h>
 
#include "../Likelihood/DataFlow/DataFlowCWise.h"
#include "SubstitutionMapping.h"
 
// From the STL:
#include <vector>
 
namespace bpp
{
class ProbabilisticSubstitutionMapping :
  public AbstractSubstitutionMapping,
  public AssociationTreeGlobalGraphObserver<PhyloNode, PhyloBranchMapping>
{
public:
  typedef AssociationTreeGlobalGraphObserver<PhyloNode, PhyloBranchMapping> mapTree;
 
private:
  PatternType rootPatternLinks_;
 
  bool usePatterns_;
 
  size_t numberOfDistinctSites_;
 
public:
  typedef mapTree::EdgeIterator EdgeIterator;
  typedef mapTree::NodeIterator NodeIterator;
 
public:
  ProbabilisticSubstitutionMapping(const PhyloTree& tree, size_t nbTypes, size_t numberOfSites) :
    AbstractMapping(numberOfSites), AbstractSubstitutionMapping(), mapTree(tree), rootPatternLinks_(), usePatterns_(false), numberOfDistinctSites_(numberOfSites)
  {
    setNumberOfSubstitutionTypes(nbTypes);
 
    std::unique_ptr<EdgeIterator> nIT = allEdgesIterator();
    for ( ; !nIT->end(); nIT->next())
    {
      (**nIT)->setNumberOfSitesAndTypes(numberOfDistinctSites_, nbTypes);
    }
  }
 
  ProbabilisticSubstitutionMapping(const PhyloTree& tree, size_t nbTypes, const PatternType& rootpatterns, size_t nbDistinctSites) :
    AbstractMapping(size_t(rootpatterns.size())), AbstractSubstitutionMapping(), mapTree(tree), rootPatternLinks_(rootpatterns), usePatterns_(true), numberOfDistinctSites_(nbDistinctSites)
  {
    setNumberOfSubstitutionTypes(nbTypes);
    std::unique_ptr<EdgeIterator> nIT = allEdgesIterator();
    for ( ; !nIT->end(); nIT->next())
    {
      (**nIT)->setNumberOfSitesAndTypes(numberOfDistinctSites_, nbTypes);
    }
  }
 
  ProbabilisticSubstitutionMapping(const PhyloTree& tree) :
    AbstractMapping(), AbstractSubstitutionMapping(), mapTree(tree), rootPatternLinks_(), usePatterns_(false), numberOfDistinctSites_(0)
  {}
 
  ProbabilisticSubstitutionMapping* clone() const override
  {
    return new ProbabilisticSubstitutionMapping(*this);
  }
 
  ProbabilisticSubstitutionMapping(const ProbabilisticSubstitutionMapping& psm) :
    AbstractMapping(psm), AbstractSubstitutionMapping(psm), mapTree(psm), rootPatternLinks_(psm.rootPatternLinks_), usePatterns_(psm.usePatterns_), numberOfDistinctSites_(psm.numberOfDistinctSites_)
  {}
 
  ProbabilisticSubstitutionMapping& operator=(const ProbabilisticSubstitutionMapping& psm)
  {
    AbstractSubstitutionMapping::operator=(psm);
    mapTree::operator=(psm);
 
    rootPatternLinks_ = psm.rootPatternLinks_;
    usePatterns_ = psm.usePatterns_;
    numberOfDistinctSites_ = psm.numberOfDistinctSites_;
 
    return *this;
  }
 
  virtual ~ProbabilisticSubstitutionMapping() {}
 
public:
  const PhyloBranchMapping& getBranch(unsigned int branchIndex) const override
  {
    return *getEdge(branchIndex);
  }
 
  PhyloBranchMapping& getBranch(unsigned int branchIndex) override
  {
    return *getEdge(branchIndex);
  }
 
  size_t getNumberOfBranches() const override
  {
    return getNumberOfEdges();
  }
 
  size_t getNumberOfDistinctSites() const
  {
    return numberOfDistinctSites_;
  }
 
  double getCount(unsigned int branchId, size_t site, size_t type) const
  {
    return getEdge(branchId)->getSiteTypeCount(getSiteIndex(site), type);
  }
 
  const std::vector<double>& getCounts(unsigned int branchId, size_t site) const
  {
    return getEdge(branchId)->getSiteCount(getSiteIndex(site));
  }
 
  void setNumberOfSitesAndTypes(size_t numberOfSites, size_t numberOfTypes);
 
  void setNumberOfSites(size_t numberOfSites) override;
 
  void setNumberOfSubstitutionTypes(size_t numberOfTypes) override;
 
  double& operator()(unsigned int branchId, size_t siteIndex, size_t type) override
  {
    return (*getEdge(branchId))(siteIndex, type);
  }
 
  void fillMappingVectorForSite(size_t siteIndex, VVdouble& counts) const;
 
  virtual const double& operator()(unsigned int branchId, size_t siteIndex, size_t type) const override
  {
    return (*getEdge(branchId))(siteIndex, type);
  }
 
  bool usePatterns() const
  {
    return usePatterns_;
  }
 
  const PatternType getPatterns() const
  {
    return rootPatternLinks_;
  }
 
  const size_t getSiteIndex(size_t site) const
  {
    return usePatterns_ ? rootPatternLinks_(Eigen::Index(site)) : site;
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_MAPPING_PROBABILISTICSUBSTITUTIONMAPPING_H