AbstractSinglePhyloSubstitutionMapping.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include "AbstractSinglePhyloSubstitutionMapping.h"
 
using namespace bpp;
using namespace std;
 
 
AbstractSinglePhyloSubstitutionMapping::AbstractSinglePhyloSubstitutionMapping(const AbstractSinglePhyloSubstitutionMapping& sppm) :
  modelTree(sppm),
  pReg_(sppm.pReg_),
  weights_(sppm.weights_),
  distances_(sppm.distances_),
  counts_(sppm.counts_ ? sppm.counts_->clone() : 0),
  factors_(sppm.factors_ ? sppm.factors_->clone() : 0),
  modelColl_(sppm.modelColl_),
  mModBrid_(sppm.mModBrid_)
{
  // assign correct addresses
  unique_ptr<modelTree::EdgeIterator> nIT = allEdgesIterator();
 
  vector<size_t> keys = modelColl_.keys();
 
  for ( ; !nIT->end(); nIT->next())
  {
    (**nIT)->pMod_ = 0;
    uint brid = getEdgeIndex(**nIT);
 
    auto sm = sppm.getEdge(brid)->pMod_;
 
    if (sm)
    {
      for (auto& k:keys)
      {
        if (sppm.modelColl_[k] == sm)
        {
          (**nIT)->pMod_ = modelColl_[k];
          break;
        }
      }
 
      if (!(**nIT)->pMod_)
        throw Exception("AbstractSinglePhyloSubstitutionMapping::AbstractSinglePhyloSubstitutionMapping: unable to find model for branch " + TextTools::toString(brid));
    }
  }
}
 
 
AbstractSinglePhyloSubstitutionMapping& AbstractSinglePhyloSubstitutionMapping::operator=(const AbstractSinglePhyloSubstitutionMapping& sppm)
{
  modelTree::operator=(sppm);
  pReg_ = sppm.pReg_;
  weights_ = sppm.weights_;
  distances_ = sppm.distances_;
 
  counts_.reset(sppm.counts_ ? sppm.counts_->clone() : 0);
  factors_.reset(sppm.factors_ ? sppm.factors_->clone() : 0);
  modelColl_ = sppm.modelColl_;
 
  mModBrid_ = sppm.mModBrid_;
 
  // assign correct addresses
  unique_ptr<modelTree::EdgeIterator> nIT = allEdgesIterator();
  vector<size_t> keys = modelColl_.keys();
 
  for ( ; !nIT->end(); nIT->next())
  {
    (**nIT)->pMod_ = 0;
 
    uint brid = getEdgeIndex(**nIT);
    auto sm = sppm.getEdge(brid)->pMod_;
 
    if (sm)
    {
      for (auto& k:keys)
      {
        if (sppm.modelColl_[k] == sm)
        {
          (**nIT)->pMod_ = modelColl_[k];
          break;
        }
      }
 
      if (!(**nIT)->pMod_)
        throw Exception("AbstractSinglePhyloSubstitutionMapping::AbstractSinglePhyloSubstitutionMapping: unable to find model for branch " + TextTools::toString(brid));
    }
  }
 
  return *this;
}
 
 
void AbstractSinglePhyloSubstitutionMapping::addModel(size_t index, const TransitionModelInterface& model, Vuint brIds)
{
  modelColl_.addObject(std::shared_ptr<TransitionModelInterface>(model.clone()), index);
 
  auto tm = modelColl_[index];
  mModBrid_[index] = brIds;
 
  for (auto& id : brIds)
  {
    auto mb = make_shared<ModelBranch>();
    mb->pMod_ = tm;
 
    associateEdge(mb, id);
  }
}