SimpleSubstitutionProcessSequenceSimulator.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include "SimpleSubstitutionProcessSequenceSimulator.h"
 
// From boo-seq:
#include <Bpp/Seq/Container/VectorSiteContainer.h>
 
using namespace bpp;
using namespace std;
 
/******************************************************************************/
 
unique_ptr<SiteContainerInterface> SimpleSubstitutionProcessSequenceSimulator::simulate(
    size_t numberOfSites) const
{
  auto seqNames = siteSim_->getSequenceNames();
  auto sites = make_unique<VectorSiteContainer>(seqNames, getAlphabet());
  sites->setSequenceNames(seqNames, true);
  for (size_t j = 0; j < numberOfSites; ++j)
  {
    auto site = siteSim_->simulateSite();
    site->setCoordinate(static_cast<int>(j));
    sites->addSite(site);
  }
  return sites;
}
 
/******************************************************************************/