void printSequences(ostream& os, AlignmentConstPtr alignment, const string& genomeName) { const Genome* genome = alignment->openGenome(genomeName); if (genome == NULL) { throw hal_exception(string("Genome ") + genomeName + " not found."); } if (genome->getNumSequences() > 0) { SequenceIteratorConstPtr seqIt = genome->getSequenceIterator(); SequenceIteratorConstPtr seqEnd = genome->getSequenceEndIterator(); for (; !seqIt->equals(seqEnd); seqIt->toNext()) { if (!seqIt->equals(genome->getSequenceIterator())) { os << ","; } os << seqIt->getSequence()->getName(); } } os << endl; }