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()));
}
bool operator<(const Site& site1, const Site& site2)
{
return site1.getPosition() < site2.getPosition();
}
Site::Site(const Site& site): BasicSymbolList(site), position_(site.getPosition()) {}