SiteContainer* SequenceSimulationTools::simulateSites(const SiteSimulator& simulator, const vector<double>& rates)
{
size_t numberOfSites = rates.size();
vector<const Site*> vs(numberOfSites);
for (size_t i = 0; i < numberOfSites; i++)
{
Site* s = simulator.simulateSite(rates[i]);
s->setPosition(static_cast<int>(i));
vs[i] = s;
}
SiteContainer* sites = new VectorSiteContainer(vs, simulator.getAlphabet());
sites->setSequencesNames(simulator.getSequencesNames(), false);
// Freeing memory:
for (size_t i = 0; i < numberOfSites; i++)
{
delete vs[i];
}
return sites;
}
SiteContainer* SequenceSimulationTools::simulateSites(const SiteSimulator& simulator, const vector<double>& rates, const vector<size_t>& states)
throw (Exception)
{
size_t numberOfSites = rates.size();
if (states.size() != numberOfSites)
throw Exception("SequenceSimulationTools::simulateSites., 'rates' and 'states' must have the same length.");
vector<const Site*> vs(numberOfSites);
for (size_t i = 0; i < numberOfSites; i++)
{
Site* s = simulator.simulateSite(states[i], rates[i]);
s->setPosition(static_cast<int>(i));
vs[i] = s;
}
SiteContainer* sites = new VectorSiteContainer(vs, simulator.getAlphabet());
sites->setSequencesNames(simulator.getSequencesNames(), false);
// Freeing memory:
for (size_t i = 0; i < numberOfSites; i++)
{
delete vs[i];
}
return sites;
}