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());
}