GivenDataSubstitutionProcessSequenceSimulator.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include "GivenDataSubstitutionProcessSequenceSimulator.h"
 
// From bpp-seq:
#include <Bpp/Seq/Container/VectorSiteContainer.h>
 
using namespace bpp;
using namespace std;
 
/******************************************************************************/
 
unique_ptr<SiteContainerInterface> GivenDataSubstitutionProcessSequenceSimulator::simulate(
    size_t numberOfSites) const
{
  if (numberOfSites > calcul_->getNumberOfSites())
    throw BadIntegerException("GivenDataSubstitutionProcessSequenceSimulator::simulate. Too many sites to simulate.", (int)numberOfSites);
 
  auto seqNames = vSiteSim_[0]->getSequenceNames();
  auto sites = make_unique<VectorSiteContainer>(seqNames, getAlphabet());
  sites->setSequenceNames(seqNames, true);
 
  for (size_t j = 0; j < numberOfSites; j++)
  {
    auto site = vSiteSim_[calcul_->getRootArrayPosition(j)]->simulateSite();
    site->setCoordinate(static_cast<int>(j));
    sites->addSite(site);
  }
  return sites;
}
 
/******************************************************************************/