vector<pair<string, string>> Alignment::_get_sequences(VectorSiteContainer *seqs) {
vector<pair<string, string>> ret;
if (!seqs) {
cerr << "Empty sequences pointer" << endl;
throw exception();
}
for (size_t i = 0; i < seqs->getNumberOfSequences(); ++i) {
BasicSequence seq = seqs->getSequence(i);
ret.push_back(make_pair(seq.getName(), seq.toString()));
}
return ret;
}
BasicSequence::BasicSequence(const BasicSequence& s) :
BasicSymbolList(s),
name_(s.getName()),
comments_(s.getComments())
{}