SingleProcessSubstitutionMapping.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include "SingleProcessSubstitutionMapping.h"
 
using namespace bpp;
using namespace std;
 
SingleProcessSubstitutionMapping::SingleProcessSubstitutionMapping(
    std::shared_ptr<SingleProcessPhyloLikelihood> spp,
    std::shared_ptr<SubstitutionRegisterInterface> reg,
    std::shared_ptr<const AlphabetIndex2> weights,
    std::shared_ptr<const AlphabetIndex2> distances,
    double threshold,
    bool verbose) :
  AbstractSinglePhyloSubstitutionMapping(spp->tree()->getGraph(), reg, weights, distances),
  pSPP_(spp)
{
  setBranchedModelSet_();
 
  // assigns edge indexes
  const auto tree = spp->tree();
 
  unique_ptr<modelTree::EdgeIterator> eIT = allEdgesIterator();
 
  for ( ; !eIT->end(); eIT->next())
  {
    auto edge1 = tree->getEdgeFromGraphid(getEdgeGraphid(**eIT));
    if (tree->hasEdgeIndex(edge1))
      setEdgeIndex(**eIT, tree->getEdgeIndex(edge1));
  }
 
  // assigns node indexes
  unique_ptr<modelTree::NodeIterator> nIT = allNodesIterator();
 
  for ( ; !nIT->end(); nIT->next())
  {
    auto node1 = tree->getNodeFromGraphid(getNodeGraphid(**nIT));
    if (tree->hasNodeIndex(node1))
      setNodeIndex(**nIT, tree->getNodeIndex(node1));
  }
}
 
 
void SingleProcessSubstitutionMapping::computeNormalizations(const ParameterList& nullParams,
    short unresolvedOption,
    bool verbose)
{
  matchParametersValues(nullParams);
 
  factors_ = SubstitutionMappingTools::computeNormalizations(
        getLikelihoodCalculationSingleProcess(),
        shared_from_this(),
        getSubstitutionRegister(),
        getDistances(),
        unresolvedOption,
        verbose);
}
 
void SingleProcessSubstitutionMapping::setBranchedModelSet_()
{
  const SubstitutionProcessInterface& sp = pSPP_->substitutionProcess();
 
  vector<size_t> vId = sp.getModelNumbers();
 
  for (auto id : vId)
  {
    addModel(id, dynamic_cast<const TransitionModelInterface&>(sp.model(id)), sp.getNodesWithModel(id));
  }
}