CollectionNodes.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include <Bpp/Phyl/Model/RateDistribution/ConstantRateDistribution.h>
 
#include "Bpp/Phyl/Likelihood/DataFlow/ProcessTree.h"
#include "CollectionNodes.h"
 
using namespace std;
using namespace bpp;
 
CollectionNodes::CollectionNodes(
    Context& context,
    shared_ptr<const SubstitutionProcessCollection> collection) :
  AbstractParametrizable(""),
  collection_(collection), context_(context)
{
  // add Independent Parameters
  const auto& paramProc = collection_->getIndependentParameters();
 
  for (size_t i = 0; i < paramProc.size(); ++i)
  {
    shareParameter_(ConfiguredParameter::create(this->context(), paramProc[i]));
  }
 
  // Share dependencies with aliased parameters
 
  for (size_t i = 0; i < paramProc.size(); ++i)
  {
    auto vs = collection_->getAlias(paramProc[i].getName());
    auto dep = dynamic_cast<const ConfiguredParameter*>(&parameter(paramProc[i].getName()))->dependency(0);
    for (const auto& s:vs)
    {
      auto newacp = ConfiguredParameter::create(this->context(), {dep}, collection_->parameter(s));
      shareParameter_(newacp);
    }
  }
 
 
  // rates nodes
  auto rN = collection_->getRateDistributionNumbers();
 
  for (auto num : rN)
  {
    std::string suff = "_" + TextTools::toString(num);
 
    auto obj = collection_->getRateDistribution(num);
 
    if (!dynamic_pointer_cast<const ConstantRateDistribution>(obj))
      distColl_.addObject(ConfiguredParametrizable::createConfigured<DiscreteDistributionInterface, ConfiguredDistribution>(this->context(), *obj, getParameters_(), suff), num);
  }
 
  // models nodes
  auto mN = collection_->getModelNumbers();
 
  for (auto num : mN)
  {
    std::string suff = "_" + TextTools::toString(num);
 
    const auto& obj = collection_->getModel(num);
 
    modelColl_.addObject(ConfiguredParametrizable::createConfigured<BranchModelInterface, ConfiguredModel>(context_, *obj, getParameters_(), suff), num);
  }
 
  // frequencies nodes
  auto fN = collection_->getFrequenciesNumbers();
 
  for (auto num : fN)
  {
    std::string suff = "_" + TextTools::toString(num);
 
    const auto& obj = collection_->frequencySet(num);
 
    freqColl_.addObject(ConfiguredParametrizable::createConfigured<FrequencySetInterface, ConfiguredFrequencySet>(context_, obj, getParameters_(), suff), num);
  }
 
  // tree nodes
  auto tN = collection_->getTreeNumbers();
 
  for (auto num : tN)
  {
    std::string suff = "_" + TextTools::toString(num);
 
    auto obj = collection_->getTree(num);
 
    treeColl_.addObject(make_shared<ProcessTree>(context_, *obj, getParameters_(), suff), num);
  }
}
 
std::shared_ptr<ProcessTree> CollectionNodes::getProcessTree(size_t treeIndex)
{
  return std::dynamic_pointer_cast<ProcessTree>(treeColl_[treeIndex]);
}