LikelihoodCalculationOnABranch.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LIKELIHOOD_DATAFLOW_LIKELIHOODCALCULATION_ON_A_BRANCH_H
#define BPP_PHYL_LIKELIHOOD_DATAFLOW_LIKELIHOODCALCULATION_ON_A_BRANCH_H
 
#include <Bpp/Graph/AssociationDAGraphImplObserver.h>
#include <Bpp/Seq/Container/AlignmentData.h>
 
#include "Bpp/Phyl/Likelihood/DataFlow/LikelihoodCalculationSingleProcess.h"
#include "Bpp/Phyl/Likelihood/DataFlow/Model.h"
#include "Bpp/Phyl/Likelihood/SubstitutionProcess.h"
 
namespace bpp
{
using LikelihoodFromRootConditionalAtRoot =
    MatrixProduct<RowLik, Eigen::RowVectorXd, MatrixLik>;
 
using TotalLogLikelihood = SumOfLogarithms<RowLik>;
 
using BuildConditionalLikelihood =
    CWiseMul<MatrixLik, std::tuple<MatrixLik, MatrixLik>>;
 
// Lower Conditional Likelihood under nodes
using ForwardLikelihoodBelow = Value<MatrixLik>;
using ForwardLikelihoodBelowRef = ValueRef<MatrixLik>;
 
// Upper Likelihood at top of edges
using BackwardLikelihoodAbove = Value<MatrixLik>;
using BackwardLikelihoodAboveRef = ValueRef<MatrixLik>;
 
using SiteLikelihoods = Value<RowLik>;
using SiteLikelihoodsRef = ValueRef<RowLik>;
 
using AllRatesSiteLikelihoods = MatrixLik;
 
using SiteWeights = NumericConstant<Eigen::RowVectorXi>;
 
using ForwardTransition =
    MatrixProduct<MatrixLik, Eigen::MatrixXd, MatrixLik>;
 
/*
 * @brief DAG of the conditional likelihoods (product of above and
 * below likelihoods), with same topology as forward & backward
 * likelihood DAGs.
 *
 */
 
 
class LikelihoodCalculationOnABranch :
  public AlignedLikelihoodCalculation
{
private:
  /* Considered Edge for each rate category */
 
  class RateCategoryEdge
  {
public:
    /* Vectors are necessary to account for all branches in the DAG matching a tree branch.
     */
 
    /* vector of Forward Conditional likelihoods at the bottom of the edge */
    std::vector<ForwardLikelihoodBelowRef> vBotLik_;
 
    /* Backward Conditional likelihood at the bottom of the edge */
 
    std::vector<BackwardLikelihoodAboveRef> vTopLik_;
 
    /* Conditional likelihoods of the edge */
 
    SiteLikelihoodsRef siteLik_;
 
    /************************************/
    /* Dependencies */
 
    std::shared_ptr<ConfiguredParameter> brlen_;
  };
 
 
  /*
   * @brief Number of sites
   *
   */
 
  size_t numberOfSites_;
 
  /*
   * @brief Dimension of the shrunked data
   */
 
  MatrixDimension likelihoodMatrixDim_;
 
  /*
   *@brief DF Model used on this branch
   *
   */
 
  std::shared_ptr<ConfiguredModel> model_;
 
 
  /*****************************
   ****** Patterns
   *
   * @brief Links between sites and patterns.
   *
   * The size of this vector is equal to the number of sites in the container,
   * each element corresponds to a site in the container and points to the
   * corresponding column in the likelihood array of the root node.
   * If the container contains no repeated site, there will be a strict
   * equivalence between each site and the likelihood array of the root node.
   * However, if this is not the case, some pointers may point toward the same
   * element in the likelihood array.
   */
 
  ValueRef<PatternType> rootPatternLinks_;
 
  std::shared_ptr<SiteWeights> rootWeights_;
 
  /*
   * @brief Node for the probabilities of the rate classes
   *
   */
 
  ValueRef<Eigen::RowVectorXd> catProb_;
 
  /* Likelihood Edges with for all rate categories */
  std::vector<RateCategoryEdge> vRateCatEdges_;
 
public:
  LikelihoodCalculationOnABranch(Context& context, LikelihoodCalculationSingleProcess& likcalsp, uint edgeId);
 
 
  void setModel(std::shared_ptr<ConfiguredModel> model)
  {
    if (model == model_)
      return;
    model_ = model;
    shareParameters_(model_->getParameters());
    makeLikelihoods();
  }
 
  LikelihoodCalculationOnABranch(const LikelihoodCalculationOnABranch& lik);
 
  LikelihoodCalculationOnABranch* clone() const
  {
    throw bpp::Exception("LikelihoodCalculationOnABranch clone should not happen.");
  }
 
  const StateMapInterface& stateMap() const
  {
    return model_->targetValue()->stateMap();
  }
 
  std::shared_ptr<const StateMapInterface> getStateMap() const
  {
    return model_->targetValue()->getStateMap();
  }
 
  std::shared_ptr<const Alphabet> getAlphabet() const
  {
    return stateMap().getAlphabet();
  }
 
 
  /************************************************
   *** Patterns
   ****************************/
 
  /*
   * @brief the relations between real position and shrunked data
   * positions.
   *
   * @param currentPosition : position in real data
   *
   * @return matching position in shrunked data
   *
   */
  size_t getRootArrayPosition(size_t currentPosition) const
  {
    return rootPatternLinks_ ? rootPatternLinks_->targetValue()(Eigen::Index(currentPosition)) : currentPosition;
  }
 
  const PatternType& getRootArrayPositions() const { return rootPatternLinks_->targetValue(); }
 
  /*
   * @brief Expands (ie reverse of shrunkage) a vector computed of
   * shrunked data (ie from one value per distinct site to one
   * value per site).
   *
   */
  ValueRef<RowLik> expandVector(ValueRef<RowLik> vector)
  {
    if (!rootPatternLinks_)
      return vector;
    else
      return CWisePattern<RowLik>::create(getContext_(), {vector, rootPatternLinks_}, RowVectorDimension ((int)numberOfSites_));
  }
 
  /*
   * @brief Expands (ie reverse of shrunkage) a matrix computed of
   * shrunked data (ie from one value per distinct site to one
   * value per site). Columns are sites.
   *
   */
  ValueRef<MatrixLik> expandMatrix(ValueRef<MatrixLik> matrix)
  {
    if (!rootPatternLinks_)
      return matrix;
    else
      return CWisePattern<MatrixLik>::create(getContext_(), {matrix, rootPatternLinks_}, MatrixDimension (matrix->targetValue().rows(), Eigen::Index (numberOfSites_)));
  }
 
  /*
   * @brief: Get the weight of a position in the shrunked data (ie
   * the number of sites corresponding to this site)
   *
   */
  unsigned int getWeight(size_t pos) const
  {
    return (uint)(rootWeights_->targetValue()(Eigen::Index(pos)));
  }
 
  std::shared_ptr<SiteWeights> getRootWeights()
  {
    return rootWeights_;
  }
 
  /********************************************************
   * @Likelihoods
   *
   *****************************************************/
 
  /*********************************/
  /* @brief Methods for external usage (after lik computation) */
 
  RowLik getSiteLikelihoodsForAClass(size_t nCat, bool shrunk = false);
 
  AllRatesSiteLikelihoods getSiteLikelihoodsForAllClasses(bool shrunk = false);
 
  size_t getNumberOfDistinctSites() const
  {
    return (size_t)likelihoodMatrixDim_.cols;
  }
 
  size_t getNumberOfSites() const
  {
    return numberOfSites_;
  }
 
  std::shared_ptr<ConfiguredModel> getModel()
  {
    return model_;
  }
 
private:
  void makeLikelihoods();
 
  std::shared_ptr<SiteLikelihoods> getSiteLikelihoods_(size_t nCat);
 
  void cleanAllLikelihoods();
};
} // namespace bpp
 
#endif // BPP_PHYL_LIKELIHOOD_DATAFLOW_LIKELIHOODCALCULATION_ON_A_BRANCH_H