void VectorSiteContainer::addSite(const Site& site, bool checkPositions) throw (Exception)
{
  // Check size:
  if (site.size() != getNumberOfSequences())
    throw SiteException("VectorSiteContainer::addSite. Site does not have the appropriate length", &site);

  // New site's alphabet and site container's alphabet matching verification
  if (site.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
  {
    throw AlphabetMismatchException("VectorSiteContainer::addSite", getAlphabet(), site.getAlphabet());
  }

  // Check position:
  if (checkPositions)
  {
    int position = site.getPosition();
    // For all positions in vector : throw exception if position already exists
    for (size_t i = 0; i < sites_.size(); i++)
    {
      if (sites_[i]->getPosition() == position)
        throw SiteException("VectorSiteContainer::addSite. Site position already exists in container", &site);
    }
  }

  sites_.push_back(dynamic_cast<Site*>(site.clone()));
}
void VectorSiteContainer::addSite(const Site& site, size_t siteIndex, int position, bool checkPositions) throw (Exception)
{
  if (siteIndex >= getNumberOfSites())
    throw IndexOutOfBoundsException("VectorSiteContainer::addSite", siteIndex, 0, getNumberOfSites() - 1);

  // Check size:
  if (site.size() != getNumberOfSequences())
    throw SiteException("VectorSiteContainer::addSite. Site does not have the appropriate length", &site);

  // New site's alphabet and site container's alphabet matching verification
  if (site.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
  {
    throw AlphabetMismatchException("VectorSiteContainer::addSite", getAlphabet(), site.getAlphabet());
  }

  // Check position:
  if (checkPositions)
  {
    // For all positions in vector : throw exception if position already exists
    for (size_t i = 0; i < sites_.size(); i++)
    {
      if (sites_[i]->getPosition() == position)
        throw SiteException("VectorSiteContainer::addSite. Site position already exists in container", &site);
    }
  }

  Site* copy = dynamic_cast<Site*>(site.clone());
  copy->setPosition(position);
  sites_.insert(sites_.begin() + siteIndex, copy);
}
void VectorSiteContainer::setSite(size_t pos, const Site& site, bool checkPositions) throw (Exception)
{
  if (pos >= getNumberOfSites())
    throw IndexOutOfBoundsException("VectorSiteContainer::setSite.", pos, 0, getNumberOfSites() - 1);

  // Check size:
  if (site.size() != getNumberOfSequences())
    throw SiteException("AlignedSequenceContainer::addSite. Site does not have the appropriate length", &site);

  // New site's alphabet and site container's alphabet matching verification
  if (site.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
    throw AlphabetMismatchException("VectorSiteContainer::setSite", getAlphabet(), site.getAlphabet());

  // Check position:
  if (checkPositions)
  {
    int position = site.getPosition();
    // For all positions in vector : throw exception if position already exists
    for (size_t i = 0; i < sites_.size(); i++)
    {
      if (sites_[i]->getPosition() == position)
        throw SiteException("VectorSiteContainer::setSite: Site position already exists in container", &site);
    }
  }
  delete sites_[pos];
  sites_[pos] = dynamic_cast<Site*>(site.clone());
}