Example #1
0
bool operator==(const Site& site1, const Site& site2)
{
	// Verify that site's size, position and content are equals
	if(site1.size() != site2.size()) return false;
	if(site1.getPosition() != site2.getPosition()) return false;
	else {
		for(unsigned int i = 0; i < site1.size(); i++) {
			if(site1[i] != site2[i]) return false;
		}
		return true;
	}
}
void VectorSiteContainer::addSite(const Site& site, size_t siteIndex, 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)
  {
    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);
    }
  }

  // insert(begin() + pos, new Site(site));
  sites_.insert(sites_.begin() + siteIndex, dynamic_cast<Site*>(site.clone()));
}
Example #3
0
bool operator<(const Site& site1, const Site& site2)
{
	return site1.getPosition() < site2.getPosition();
}
Example #4
0
Site::Site(const Site& site): BasicSymbolList(site), position_(site.getPosition()) {}